Objective: To evaluate whether first trimester screening markers are altered in pregnancies affected both by other chromosomal defects than trisomy 21 and structural anomalies and whether it is possible to detect these pregnancies by combined ultrasound and biochemical screening test. Methods: Altogether 4,776 singleton pregnancies underwent first trimester screening. Of them, 3,101 women were screened using a combination of maternal serum free hCG, pregnancy-associated plasma protein A and nuchal translucency and 1,361 women with first trimester biochemistry without ultrasound. Nuchal translucency screening was performed between the 11th and 13+6th gestational weeks, and biochemistry 1–2 weeks earlier. Results: Using a fixed cut-off rate of 1:250 for Down’s syndrome, the detection rate of trisomies 21, 18 and 13 were 92, 67 and 0%, respectively. All open defects, 85% of cardiac defects and other minor defects were not detected in first trimester screening. Majority of these structural abnormalities occurred in women under 35 years of age. Conclusion: First trimester Down’s syndrome screening is effective in trisomy screening, but its performance in structural abnormalities is low, when used as a part of routine clinical practice. We conclude that it is too early to drop second trimester screening ultrasound entirely from antenatal care programs if a high detection rate is to be achieved also in structural defects.