The purpose of the present study was to examine screening marker levels in Down syndrome (DS) pregnancies with and without cardiac defects and in euploid pregnancies. Retrospective series in two centers with one or more markers—ultrasound nuchal translucency (NT), first trimester maternal serum pregnancy associated plasma protein (PAPP-A), free-β human chorionic gonadotrophin (free β-hCG), and second trimester serum α-fetoprotein (AFP), unconjugated estriol (uE 3 ), hCG, and free-β hCG. Levels were expressed as multiples of the gestation-specific median (MoM). Differences were assessed by the Wilcoxon rank sum test and 95 % confidence intervals. There were 318 DS pregnancies including 53 (17 %) with cardiac defects. Median NT was higher in cardiac defects (1.82 compared with 1.62 MoM), but not statistically significant ( P = 0.17). Median free β-hCG was significantly highly reduced in the first trimester (1.14 and 2.17 MoM; P < 0.005) and similarly but nonsignificantly in the second trimester (1.59 and 2.32 MoM; P = 0.14). PAPP-A was reduced and AFP increased nonsignificantly with no material differences for uE 3 and hCG. The results on NT and free β-hCG were consistent with a series of 62 euploid pregnancies with cardiac defects screened in one of the centers. The distribution of some markers differs in DS pregnancies with cardiac defects. Depending on the screening protocol, this may affect the phenotype of DS births.