Introduction Prenatal exposure to ortho-phthalates has been suggested as a possible risk factor for Autism Spectrum Disorders (ASD) through their anti-androgenic activity. In rats, prenatal exposure to phthalates causes hypospadias (abnormal positioning of the urethral opening) and cryptorchidism (undescended testis), two common male reproductive tract disorders. An ecological analysis of human newborn infants showed a strong correlation between these two disorders and ASD, but this association has not been extensively studied on an individual level. Methods We analyzed all male singleton live births (n=147,171) from January 1, 1999 through December 31, 2008 occurring in a large Israeli healthcare organization. Boys with cryptorchidism (n=3,649) or hypospadias (n=2,342) were identified via ICD-9 codes. ASD cases (n=1,329) were identified by ICD-9 code and verified by review of medical records. Analyses were conducted using generalized additive mixed effect models with random component accounting for family clusters. Results In multivariable-adjusted analyses, the odds ratio (OR) for ASD among boys with hypospadias or cryptorchidism was 1.31 (95% confidence interval (CI): 1.01-1.68). For cryptorchidism only the OR was 1.44 (95% CI: 1.06-1.96) and for hypospadias only was 1.07 (95% CI: 0.70-1.64). Restricting to boys who underwent surgical correction strengthened the results for cryptorchidism (OR: 1.77; 95% CI: 1.16-2.72), but not hypospadias. Conclusions Boys with cryptorchidism were at higher risk of ASD, but we did not observe an increased risk among boys with hypospadias. Differences in ASD risk between the disorders may reflect variations in critical windows of exposure to a hypoandrogenic in-utero environment, or effects of other singling systems involved in the etiology of the disorders. Understanding the links between cryptorchidism and ASD could shed light on mechanisms of ASD pathogenesis.