[Doctor's Explanation] Can NIPT Reveal the Baby's Sex?

Revised: January 15, 2026

NIPT analyzes cell-free fetal DNA (cffDNA) in maternal blood, and by detecting the presence or absence of the Y chromosome, it can determine the fetus's sex around the 10th week of pregnancy with about 99% accuracy. However, since accuracy can vary depending on factors such as gestational week, BMI, and twin pregnancy, correct understanding is important.

The baby's sex is one of the topics that many expectant mothers become curious about from early pregnancy. In recent years, information that "NIPT can reveal the sex early and accurately" has spread, and more people want to know sooner than what an ultrasound can offer.

In fact, because NIPT analyzes fetal-derived DNA (cell-free fetal DNA: cffDNA), sex determination accuracy is extremely high. cffDNA is a fragment of DNA released from placental chorionic villus cells into the maternal blood during pregnancy, and by decoding it using next-generation sequencing (NGS) technology, fetal genetic information can be obtained non-invasively. However, there are exceptions and points to be aware of.

In this article, from a doctor's perspective, we will clearly explain how NIPT determines fetal sex, cases that require caution, and points to know before testing. We aim to support those curious about the baby's sex so they can consider testing with peace of mind based on accurate information. For those wondering "Is it really accurate?" or "Can it be wrong?" regarding NIPT sex determination, we provide evidence-based answers, so please read to the end.

How NIPT Determines Sex — How the Y Chromosome Is Detected

During pregnancy, fragments of cffDNA flow into the maternal blood via the placenta. NIPT was originally developed to assess chromosomal abnormalities (trisomy 21, 18, 13, etc.), but in this process, it can also determine with high accuracy the presence or absence of the Y chromosome, which is related to fetal sex determination [ref:1].

The Basic Principle of Sex Determination

The logic behind sex determination is simple.
If the Y chromosome is detected, the fetus is "male"; if not detected, the fetus is "female."
Human sex chromosomes are configured as XX for females and XY for males. Since the mother is XX (female), Y-chromosome-derived DNA sequences are normally not present in maternal blood. When fetal-derived cffDNA becomes mixed in, whether a sequence unique to the Y chromosome (such as the SRY gene region) is detected allows for highly accurate estimation of the fetal sex.

Because the Y chromosome is not present in the mother, this difference enables highly accurate estimation. In fact, many studies report that the accuracy of sex determination is around 99% [ref:1]. This level of accuracy is very high compared to conventional ultrasound-based sex determination.

Differences from Ultrasound Examination

Sex determination by ultrasound is generally possible from around the 16th to 18th week of pregnancy onward, and it can be difficult to judge depending on the fetus's position and the stage of genital development. For example, if the fetus has its legs closed or the umbilical cord is near the genitals, accurate determination from the ultrasound image alone can be difficult. On the other hand, NIPT can estimate sex with high accuracy from around the 10th week of pregnancy, which is a major difference [ref:3].

Furthermore, an important feature of NIPT is that it is a non-invasive test completed with just a blood draw, so there is no risk to the mother or fetus. Unlike invasive tests such as amniocentesis, genetic information can be obtained without the risk of miscarriage, allowing the test to be taken with peace of mind.

＼The baby's sex can be known from as early as 6 weeks of pregnancy／

The Scope of Sex Determination and "Cases Requiring Caution with Results"

NIPT allows for highly accurate sex estimation, but the same accuracy is not obtained in every pregnancy. Results are affected by the amount of cffDNA and by pregnancy and maternal conditions. A certain minimum amount of cffDNA is required, and if this is insufficient, the stability of Y-chromosome detection decreases. Here, we explain in detail the representative cases where caution is needed regarding sex determination results.

When the Gestational Week Is Too Early

In early pregnancy, the amount of cffDNA tends to be low, and if testing is performed without obtaining a sufficient amount, sex determination may be withheld or retesting may be required. The amount of cffDNA increases as the gestational weeks progress, and generally once pregnancy passes 10 weeks, the fetal fraction reaches 4% or more, allowing stable test results to be obtained. However, since there are individual differences, it is important to follow the minimum gestational week recommended by the testing facility.

When the Mother's BMI Is High

If the mother's BMI is high, maternal-derived DNA increases, which relatively lowers the fetal fraction (the proportion of cffDNA), potentially reducing the accuracy of sex determination [ref:2].
This is because the higher the body fat mass, the greater the amount of cell-free DNA released due to maternal cell breakdown. As a result, it has been reported that the rate of "indeterminate results" or "retesting" increases. Those with a BMI of 30 or higher are advised to consult with the testing facility in advance and undergo testing in an environment where fetal fraction can be sufficiently confirmed.

Unique Cases Such as Disorders of Sex Development

In rare cases, when a genetic disorder of sex development (DSD) is present, the chromosomal sex and the development of external genitalia may not match [ref:1].
For example, in androgen insensitivity syndrome (AIS), the chromosomes are XY (genetically male), but the external genitalia develop as female. In such special cases, there remains a possibility that the NIPT determination differs from the sex of the external genitalia at birth. However, such cases are extremely rare, and in typical pregnancies, NIPT's sex determination can be considered extremely reliable.

In the Case of Twin Pregnancy

In twin pregnancies, cffDNA from both babies is detected mixed together, so if a Y chromosome is present, it can only be determined that "at least one is male."
There is a limitation in that the individual sex cannot be determined. In the case of identical twins, since they are genetically identical, the sex is also the same, but in the case of fraternal twins, each may be a different sex, and NIPT alone cannot distinguish the sex of each individual fetus.

Vanishing Twin Cases

Caution is also needed in cases of a "vanishing twin," where the pregnancy was a twin pregnancy in the early stage, but one fetus naturally disappears. If the cffDNA of the vanished fetus remains in the maternal blood, a Y chromosome may be detected, which could affect the sex determination of the single fetus that is actually born. In such cases, thorough discussion with a doctor is essential when interpreting the NIPT results.

As described above, while NIPT is an excellent means of sex estimation, there are cases requiring caution depending on maternal conditions and pregnancy circumstances, so it is important to maintain a flexible attitude toward accepting the results. It is important to understand that NIPT is ultimately a screening test, not a definitive diagnosis.

Pros and Cons of Learning the Sex via NIPT — For a Decision You Won't Regret

Pros

Because the sex can be known from as early as 10 weeks of pregnancy, there are benefits such as the following.

• Being able to start preparing for the birth early (selecting baby items, arranging the room, etc.)
• Making it easier to consider name candidates (narrowing down candidates once the sex is decided)
• Making it easier to smoothly inform family and those around you
• May be useful for risk assessment of sex-linked hereditary disorders (such as X-linked genetic disorders)

In particular, for women who are carriers of X-linked genetic disorders such as hemophilia or Duchenne muscular dystrophy, knowing early whether the fetus is male can be very helpful in planning subsequent detailed testing and genetic counseling [ref:4].

Cons

However, there are several important points to consider.

1. Taking NIPT solely to learn the sex is not recommended
   NIPT is originally a screening test for assessing chromosomal abnormalities, and sex determination is secondary information from it.
   Undergoing an expensive test only to learn the sex is not reasonable either medically or in terms of cost-effectiveness. NIPT generally costs anywhere from several tens of thousands to over a hundred thousand yen, so if the sole purpose is to learn the sex, the financial burden becomes significant.
2. Psychological impact
   A sex result that differs from expectations can cause psychological upset. While hoping for a particular sex is natural, the "lack of mental preparation" that comes from knowing early can sometimes become an issue. In particular, if a specific sex was strongly desired due to family or cultural background, it may take time to come to terms with a differing result. Consider using genetic counseling or psychological support as needed [ref:5].
3. Some facilities do not disclose the sex
   A particularly important point concerns institutional policy. At certified facilities in Japan, it is generally standard practice not to notify the sex, out of ethical consideration.
   This is based on ethical guidelines aimed at preventing sex-selective abortion. On the other hand, non-certified facilities may provide detailed information including the sex, and policies vary greatly by facility.
   It is essential to confirm before testing whether "the sex will be disclosed."

＼Along with the sex, genetic tendencies related to constitution and talent can also be revealed／

How Accurate Is NIPT's Sex Determination? — An Evidence-Based Explanation

Evidence regarding the accuracy of NIPT sex determination has accumulated through multiple large-scale studies. A systematic review published in 2019 showed that both the sensitivity and specificity of NIPT sex determination exceed 99% [ref:1]. This means that, compared with conventional ultrasound-based sex determination (about 95–100% even in mid-pregnancy or later), NIPT achieves equal or greater accuracy at a much earlier stage.

Main Factors Affecting Accuracy

The main factors affecting NIPT sex determination accuracy are as follows.

• Fetal fraction (proportion of fetal-derived DNA): generally 4% or more is required
• Gestational week: 10 weeks or later is recommended
• Maternal BMI: fetal fraction tends to decrease with high BMI

By taking these factors into account and undergoing testing at the appropriate timing, the reliability of sex determination can be maximized [ref:2]. Accuracy may vary slightly depending on age as well, but as far as sex determination is concerned, the effect of age is said to be relatively small [ref:3].

What Are Cases Where Sex Determination "Is Wrong"

Cases where NIPT's sex determination turns out to be "wrong" are extremely rare, but cannot be said to be completely zero [ref:4]. Specifically, the causes cited include the aforementioned vanishing twin, disorders of sex development, and insufficient fetal fraction. Also, although extremely rare, there remains some possibility of specimen mix-ups or errors in the testing process, so it is important to choose a reliable testing facility. If the NIPT sex result differs from the ultrasound result, we recommend consulting your doctor and undergoing additional evaluation.

NIPT Can Reveal Sex with High Accuracy — But It's Important to Understand the Purpose Before Testing

NIPT can estimate sex with very high accuracy through cffDNA analysis. Being able to know from early pregnancy is a major benefit, but because there are limits to accuracy depending on gestational week, maternal conditions, twin pregnancy, and other factors, it is not 100% guaranteed.

Also, if knowing the sex itself becomes the goal, it can lead to financial and psychological burdens. NIPT was originally developed mainly as a screening test for chromosomal abnormalities, including Down syndrome (trisomy 21). Sex information is only obtained as a secondary result, and it is important to undergo testing with a correct understanding of this point.

What matters most is understanding the true purpose of NIPT — the assessment of chromosomal abnormalities — and choosing to be tested with full understanding and consent. It is recommended to receive genetic counseling before testing and to receive a thorough explanation of the significance of the test, the risks, and how to interpret the results [ref:5].

Organizing the necessary information correctly and accepting the results in the way that is most convincing for you and your family will lead to a pregnancy you won't regret. For those curious about the sex, we recommend first understanding the overall purpose and significance of NIPT testing and choosing a trustworthy testing institution.

Frequently Asked Questions

Q1. From how many weeks can NIPT reveal the sex?

A. Generally, NIPT can determine the sex from around the 10th week of pregnancy. From this period onward, when the amount of cffDNA (fetal-derived DNA) has sufficiently increased, the presence or absence of the Y chromosome can be detected with high accuracy. However, since the recommended minimum gestational week may vary by testing facility, please confirm in advance. At seeDNA, sex testing is available from as early as 6 weeks of pregnancy.

Q2. How accurate is NIPT sex determination?

A. The accuracy of NIPT sex determination is at a very high level of around 99% [ref:1]. Both sensitivity and specificity are high, and reliable results can be obtained at an earlier stage than with ultrasound. However, accuracy may vary under conditions such as insufficient fetal fraction or other special circumstances.

Q3. Can NIPT sex determination be wrong?

A. It is extremely rare, but cases where the sex determination differs from the actual sex are not zero. The main causes cited include a vanishing twin (where one of an initial twin pregnancy disappears), disorders of sex development, and insufficient fetal fraction. If the ultrasound result and the NIPT result do not match, we recommend consulting your doctor and undergoing additional evaluation.

Q4. Is it possible to learn only the sex through NIPT?

A. Some facilities offer plans limited to sex determination alone. However, NIPT is originally a test intended for screening chromosomal abnormalities, and sex determination is secondary information from it. At certified facilities in Japan, it is common not to disclose the sex out of ethical consideration, but non-certified facilities and specialized institutions such as seeDNA may provide sex information in some cases. Please confirm the facility's policy before testing.

Q5. In the case of twins, can NIPT determine the sex of each individually?

A. In a twin pregnancy, if a Y chromosome is detected by NIPT, it can be determined that "at least one is male," but the sex of each fetus cannot be determined individually. In identical twins, the sex is the same, but in fraternal twins, NIPT alone cannot distinguish between them. Auxiliary means such as ultrasound are needed for individual sex determination.

Q6. Does a high BMI affect NIPT sex determination?

A. Yes, it may have an effect. If the mother's BMI is high, the amount of maternal-derived cell-free DNA increases, which relatively lowers the proportion of cffDNA (fetal-derived DNA) [ref:2]. As a result, the fetal fraction may not reach the threshold required for testing, increasing the risk of an "indeterminate result" or "retesting." Those with a BMI of 30 or higher are advised to consult with the testing facility in advance.

[References]