Cryptorchidism is the most frequent congenital malformation in boys and is associated with low sperm count, infertility and testicular cancer. Unhealthy maternal lifestyle during pregnancy such as smoking, high prepregnancy body mass index (BMI) as well as alcohol and caffeine intake may constitute possible risk factors for cryptorchidism, but results from the few previous studies are conflicting. We aimed to explore the association between maternal lifestyle factors and occurrence of cryptorchidism in sons. The Danish National Birth Cohort and the Aarhus Birth Cohort provided information on maternal lifestyle from early pregnancy. Data were linked to several Danish health registers, multiple imputation was used to handle missing data and Cox proportional hazards models were used to adjust for potential confounders. In total, 85,923 boys were included, and of them, 2.2% were diagnosed with cryptorchidism. We observed the strongest associations between maternal tobacco smoking and prepregnancy BMI and cryptorchidism. Sons of women who smoked 10-14 cigarettes/day had the highest hazard ratio (HR) for cryptorchidism (1.37; 95% CI: 1.06-1.76), and for maternal BMI ≥30 kg/m , the HR was 1.32 (95% CI: 1.06-1.65). Binge drinking was associated with an HR <1, if the women had one or two episodes in pregnancy (HR: 0.81; 95% CI: 0.67-0.98). Average maternal alcohol intake and caffeine intake during pregnancy were not significantly associated with a higher occurrence of cryptorchidism detected at birth or later in life. Maternal tobacco smoking, overweight and obesity in pregnancy were associated with higher occurrence of cryptorchidism in boys in this study.