How accurate is prenatal genetic testing? It depends on what you're testing for.
The accuracy of prenatal genetic testing is not a single number—it varies dramatically depending on the specific condition being screened. The most common and well-studied use of noninvasive prenatal testing (NIPT) is for Down syndrome (trisomy 21). In a large study of over 20,000 pregnancies, NIPT had a positive predictive value (PPV) of 71% for trisomy 21, meaning that when the test said 'positive,' there was a 71% chance the baby truly had the condition [4]. This is considered high enough to guide clinical decisions, but it also means that about 29% of positive results were false alarms. For other conditions, the accuracy was much lower: the PPV for trisomy 18 was 50%, for sex chromosome abnormalities it was 46%, and for trisomy 13 it was only 11% [4]. This means that for every 100 positive NIPT results for trisomy 13, only about 11 would be true positives—the rest would be false positives. These numbers come from one of the largest studies in this set, and they highlight a critical point: the test's reliability is condition-specific, and a positive result for a rare condition is far more likely to be wrong than a positive result for a common one.
NIPT is a screening test, not a diagnostic test—confirmatory testing is still essential.
A key distinction that directly affects clinical decisions is that NIPT is a screening test, not a diagnostic one. This means it can indicate a higher risk, but it cannot definitively diagnose a condition. The same large study that found high accuracy for trisomy 21 also emphasized that NIPT 'cannot replace prenatal diagnosis' [4]. This is because false positives and false negatives do occur. For example, in a study of NIPT for sex chromosome aneuploidies (like Turner syndrome), only about 47% of positive NIPT results were confirmed by diagnostic testing (amniocentesis or CVS) [3]. Furthermore, that study found that the majority of women (65.7%) who received a positive NIPT result for a sex chromosome condition declined confirmatory diagnostic testing, even when ultrasound findings were also suggestive of a problem [3]. This is a concerning trend because without confirmation, a woman might make a life-altering decision—such as terminating a pregnancy—based on a test result that could be wrong. The authors of that study strongly recommend that comprehensive counseling address the importance of confirmatory testing [3]. In short, NIPT is accurate enough to guide decisions about whether to pursue further testing, but it is not accurate enough to guide irreversible decisions on its own.
NIPT can also detect unexpected health problems in the mother, not just the baby.
An important and often surprising finding is that NIPT can sometimes reveal a serious health condition in the pregnant woman herself, rather than in the fetus. Because NIPT analyzes cell-free DNA from the mother's blood, it can pick up DNA from an undiagnosed cancer in the mother. In a nationwide Dutch study of over 230,000 pregnant women, about 0.02% of NIPT results raised suspicion for a maternal malignancy [1]. While this is a very low percentage, when the NIPT profile showed multiple chromosomal abnormalities (a specific pattern), the risk of a confirmed cancer was much higher—about 70% [1]. In total, 18 women were diagnosed with cancer after a suspicious NIPT result, most commonly blood cancers like lymphoma [1]. This means that in rare cases, an abnormal NIPT result can guide a clinical decision not about the pregnancy, but about the mother's own health, prompting urgent oncologic examination. This finding underscores that NIPT results must be interpreted carefully, as they can have implications for both the fetus and the mother.
About These Sources
This answer is built on 5 peer-reviewed studies — published from 2019 to 2024, 1 from 2024 or later, 2 in Q1 journals, collectively cited 73 times — selected as the most relevant from 8 studies that passed quality screening, drawn from 55 papers retrieved from a database of over 500 million.
Sources used in this answer
Noninvasive Prenatal Test Results Indicative of Maternal Malignancies: A Nationwide Genetic and Clinical Follow-Up Study
In a nationwide Dutch study of 231,896 pregnant women, 0.02% of NIPT results were suspicious for maternal malignancy; when multiple chromosomal aberrations were found, the risk of confirmed cancer was 69.6% (16/23), predominantly hematologic cancers.
Reducing decisional conflict in decisions about prenatal genetic testing: the impact of a dyadic intervention at the start of prenatal care.
In a cluster-randomized controlled trial (n=502), a shared decision-making tool (NEST) significantly reduced decisional conflict about prenatal genetic testing at follow-up compared to the control group (β -3.889, p=0.027).
Clinical experience with sex chromosome aneuploidies detected by noninvasive prenatal testing (NIPT): Accuracy and patient decision-making.
In a retrospective cohort of 136 positive NIPT results for sex chromosome aneuploidies, only 46.9% (30/64) were confirmed by diagnostic testing, and 65.7% of patients declined confirmatory testing.
The accuracy and feasibility of noninvasive prenatal testing in a consecutive series of 20,626 pregnancies with different clinical characteristics
In a study of 20,626 pregnancies, NIPT showed 100% sensitivity for trisomies 21, 18, and 13, but positive predictive values varied widely: 71% for T21, 50% for T18, and only 11% for T13.
Experience in prenatal genetic testing and reproductive decision-making for monogenic disorders from a single tertiary care genetics clinic in a low-middle income country
In a low-middle income country cohort of 40 couples at risk for monogenic disorders, 71% underwent chorionic villus sampling (mean 13.6 weeks), and 18% of fetuses were found to be affected, leading to termination of pregnancy.