ABSTRACTIntroductionGenome‐wide non‐invasive prenatal testing (gwNIPT) has screening limitations for detectable chromosomal conditions and cannot detect microdeletions/microduplications (MD) or triploidy. Thickened nuchal translucency (NT) only detects around 10% of these cases.MethodsA 4‐year retrospective study of singleton pregnancies undergoing first‐line gwNIPT screening with subsequent CVS or amniocentesis. All MD cases, with or without gwNIPT screening, were also analyzed.ResultsAmong 919 pregnancies with gwNIPT and invasive testing, 338 had a single chromosomal abnormality, with 9 false negative gwNIPT results (2.9%) and 26 undetectable abnormalities (18 MD, 8 triploidy) (7.7%). Twelve cases had a dual chromosomal abnormality and 4 returned a low‐risk gwNIPT result. Only three (9%) of the “missed cases” had a large NT and two of these also had a structural abnormality. Approximately 90% of chromosomal anomalies missed by gwNIPT were detected by invasive prenatal testing indicated by one or more of the following: failed NIPT (9%), low PAPP‐A (12%), early growth restriction (37%) and structural anomalies at pre‐NIPT, 13‐ or 20‐week ultrasounds (51%).ConclusionMost chromosomal abnormalities missed or unable to be found by gwNIPT are detected due to growth restriction or structural anomalies, not an enlarged NT. Failed NIPT and low PAPP‐A concentrations contributed to detection.