This study was undertaken to investigate the association between uterine anomalies and unexplained elevated maternal serum alpha-fetoprotein (MSAFP) concentrations during the early second trimester. The incidence of uterine anomalies was retrospectively evaluated among pregnant women showing elevated (> 2.5 multiples of the median) mid-trimester maternal serum AFP (N = 312) concentrations in otherwise normal singleton pregnancies and then compared with that amongst patients from the same clinic showing normal serum AFP results (N = 28410). Basic clinical data of the study group were also analysed. The rate of diagnosed developmental uterine malformations in patients showing elevated MSAFP levels was 1 in 31, whereas the rate in the control group was 1 in 710 (3.2 per cent vs. 0.14 per cent). The relative risk was 22.1 [95 per cent confidence interval (CI) 11.1-43.7]. Amniotic fluid (AF) concentrations of AFP were normal in the study group. Our preliminary observations suggest that elevated MSAFP in the second trimester may in some cases be explained as being solely a result of uterine anomaly. The fetal to maternal transfer of AFP occurs by a transplacental, not a transamniotic, route, since AFAFP concentrations were normal. Consequently, obstetricians taking care of these patients should take this possibility into account.