2026.05.06
NIPT (Non-Invasive Prenatal Testing) determines fetal sex with about 99% accuracy, but it can occasionally be wrong. This article clearly explains the 5 causes of sex-determination errors (such as vanishing twin syndrome).
How does NIPT determine sex?
Once you become pregnant, it's only natural to want to know your baby's sex as soon as possible. NIPT (Non-Invasive Prenatal Testing) is known as a chromosomal abnormality screening test, but it can also determine the fetus's sex with high accuracy at the same time.
NIPT analyzes tiny placenta-derived DNA fragments known as "cell-free fetal DNA (cffDNA)" contained in the mother's blood. The analysis uses a device called a next-generation sequencer, which examines millions of DNA fragments at once. Specifically, if a Y-chromosome-specific base sequence (such as the SRY gene) is detected among these DNA fragments, the result is "male"; if it is not detected, the result is "female."
Unlike observation of the external genitalia via ultrasound, a major feature of NIPT is that it can be performed as early as around 10 weeks of pregnancy.
How accurate is NIPT's sex determination? What's the chance it's correct?
In short, NIPT's sex-determination accuracy is very high, but misjudgments (errors) can occur on rare occasions.
According to a large-scale study from 2017, the accuracy of NIPT sex determination is reported as follows.
- Sensitivity (the rate at which an actual male fetus is correctly identified as male): 98.9%
- Specificity (the rate at which an actual female fetus is correctly identified as female): 99.6%
While the accuracy is extremely high at about 99%, misjudgments are not reduced to zero entirely, and as the number of tests increases, a certain number of errors can theoretically occur. Other research also reports that the rate of disagreement between NIPT and ultrasound results is around 0 to 0.9%. The key point here is that NIPT is not a "definitive diagnostic test" but rather a "screening test".
Does NIPT sometimes give a different sex than an ultrasound? 5 causes of misjudgment
Why does NIPT, despite its high accuracy, sometimes get the sex wrong? The main causes fall into the following five categories.
| Cause | Misjudgment pattern | Mechanism and details |
|---|---|---|
| 1. Low Fetal Fraction (FF) | Male fetus misjudged as "female" | When the proportion of cffDNA in the mother's blood (FF) is low (due to early gestational age, high maternal body weight, etc.), detection of the Y chromosome becomes unstable. |
| 2. Placental mosaicism | Male fetus misjudged as "female" | A phenomenon in which the chromosomal makeup of the placenta differs from that of the fetus. Since NIPT examines placenta-derived DNA, if the placenta lacks a Y chromosome, the result is judged as female. |
| 3. Vanishing twin syndrome | Female fetus misjudged as "male" | A phenomenon in which one of a pair of twins is lost early in pregnancy. Y-chromosome DNA from the lost male twin can remain in the mother's blood and be detected. |
| 4. Structural abnormalities/translocation of the Y chromosome | Male fetus misjudged as "female" | Cases such as a fetus in which the SRY gene has translocated to the X chromosome. Because the translocated fragment is too small, Y-chromosome-derived DNA is not detected. |
| 5. Maternal factors | Female fetus misjudged as "male" | Cases such as the mother herself being a chimera (46,XX/46,XY), meaning Y-chromosome-derived DNA is already present in the mother's blood. |
*In particular, in cases of vanishing twin pregnancies, some reports indicate that the rate of disagreement between NIPT sex determination and ultrasound results can reach as high as 0.8 to 10.2%.
What to do if you're worried about your NIPT results
NIPT's sex determination has both sensitivity and specificity of about 99%, making it highly accurate, but factors such as vanishing twin syndrome, placental mosaicism, and low FF can occasionally cause the result to be wrong.
NIPT is, after all, a screening test. If you have doubts about your test result, or if the sex stated in a later ultrasound differs from the NIPT result, please do not simply take the result at face value — be sure to consult your doctor. If necessary, it is recommended to confirm with a definitive diagnostic test such as amniocentesis. By correctly understanding the test's limitations and mechanisms, you can enjoy your pregnancy with peace of mind.
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FAQ (Frequently Asked Questions)
Q1. From when can NIPT tell the baby's sex?
A. It can be determined from a relatively early stage, around 10 weeks of pregnancy.
Q2. What is the probability that NIPT gets the sex wrong?
A. A 2017 study reported a sensitivity of 98.9% and specificity of 99.6%, giving an accuracy of about 99%. However, cases where results disagree with ultrasound have been reported at a rate of about 0 to 0.9%, so it is not 100%.
Q3. NIPT said "girl," but the ultrasound said "boy." Why does this happen?
A. A low Fetal Fraction (the proportion of fetal DNA in the mother's blood), placental mosaicism, structural abnormalities of the Y chromosome, and other factors can cause a Y chromosome not to be detected by NIPT even though the fetus is actually male, resulting in a "female" determination. If you have any doubts, please consult your doctor.
[References]
[1] BJOG. 2017 Jan.[2] American Journal of Obstetrics & Gynecology. 2021.
[3] The Journal of Maternal-Fetal & Neonatal Medicine. 2017 Jan.
[4] ScienceDirect. 2020.
[5] Prenatal Diagnosis. 2023.
[6] Journal of the Endocrine Society. 2025 Feb.
[7] LabCorp/Sequenom Laboratories. 2019.
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Author
M.D., Ph.D.
Tasuku Hiroshige
Doctor of Medical Science; Specialist and Instructor of the Japanese Urological Association; Certified Physician of the Japanese Society of Medical Oncology; Specialist of the Japanese Society of Anti-Aging Medicine; Japan Medical Association Certified Occupational Physician; Certified Physician of the Japanese Society of Chemotherapy; Certified Physician of the Japanese Society for Sexually Transmitted Diseases; Certificate of da Vinci system Training As a Console Surgeon, and other qualifications.
After graduating from Kagoshima University Faculty of Medicine in 2010, he has built extensive clinical experience as a urologist. Beyond his clinical duties, he is also actively engaged in academic activities such as presenting at conferences, writing papers, and securing research funding. In addition to his specialty and instructor qualifications in urology, he holds certifications across a wide range of fields including cancer treatment, anti-aging medicine, and infectious disease treatment. Drawing on his extensive medical knowledge and skills, he provides care tailored to each individual patient.