In this study, maternal smoking during pregnancy was found to be linked with lower occurrence of hypospadias but uncontrolled confounding could not be excluded. The other explored maternal lifestyle factors were not related to hypospadias in sons.

• This cohort study included 85,923 live-born singleton boys of whom 502 (0.6%) were diagnosed with hypospadias.

• A lower occurrence of hypospadias was found in relation to maternal smoking in early pregnancy.

• An increase of one cigarette smoked per day was found to be linked with lower risk of having a son with hypospadias (adjusted hazard ratio 0.97).

• Sub-analyses indicated that the findings may be prone to unadjusted confounding.

• No link was found between pre-pregnancy BMI, alcohol intake, binge drinking, or caffeine intake and hypospadias.