Previous studies have observed an increased risk of approximately twofold or more for neural tube defects (NTD) associated with maternal obesity before pregnancy based on a body mass index (BMI) of > 29 kg/m2. No additional maternal factor appeared substantially to influence this association. Here, we explore further the association between BMI and NTD risk by considering the separate contributions of maternal prepregnant BMI and height. We also explore whether selected congenital anomalies, in addition to NTDs, were associated with maternal height or prepregnant BMI. Data were derived from two California population-based case–control studies. One study comprised 538 NTD cases and 539 non-malformed control infants. The other study included an additional 265 NTD cases, as well as 207 conotruncal cases, 165 limb anomaly cases, 662 orofacial cleft cases and 734 non-malformed controls. Maternal interviews in both studies elicited information on maternal height and prepregnant weight. Anomaly risk was described using additive linear logistic regression models. Results revealed increasing NTD risk with increasing maternal prepregnant BMI, controlling for maternal height. These patterns were observed overall as well as for most race/ethnic groups. Increasing NTD risk for decreasing height controlling for maternal BMI was also observed in one NTD study, but was not as evident in the other. Elevated risks for increasing maternal BMI and decreasing maternal height were not observed consistently for the other studied anomalies. The mechanisms underlying the association between maternal weight, or possibly maternal height, and NTD-affected pregnancy risk are unknown. Exploration of other data sets will be needed to determine whether similar patterns of NTD risk or lack of risk for other anomalies are associated with the two maternal anthropometric variables, height and prepregnant weight.