Purpose To investigate associations between maternal use of selected medications during early pregnancy and the risk of hypospadias in male infants. Methods We used data from the National Birth Defects Prevention Study, a multi-site, population-based, case-control study. We analyzed data from 1,537 case infants with second or third degree isolated hypospadias and 4,314 male control infants born from 1997-2007. Exposure was based on reported use of any prescription or over-the-counter medication or herbal product, for which there were at least 5 exposed cases, from 1 month before to 4 months after conception, excluding topicals, vitamins, minerals, and products for which the components were unknown. Adjusted odds ratios (aORs) and 95% confidence intervals (CI) were estimated using multivariable logistic regression, adjusting for several confounders. Results Of the 195 medication components with at least 5 exposed cases, 89 components met the inclusion criteria and were assessed-28 herbal and 61 non-herbal components. Hypospadias was associated with reported use of cephalexin (aOR 3.06; 95% CI 1.02, 9.18), phenylpropanolamine HCl (aOR 2.68; 95% CI 1.06, 6.80), and ibuprofen (aOR 1.16; 95% CI 1.00, 1.34), in primary analyses. Conclusions We replicated a previously observed association between maternal exposure to phenylpropanolamine HCl and hypospadias. The associations with cephalexin and ibuprofen have not previously been reported. Given the exploratory nature of the analyses, these results should be considered hypothesis-generating. Better understanding of the potential fetal effects will allow clinicians and women of childbearing age to make more informed decisions regarding the use of medications during pregnancy.