Background: The intrauterine milieu plays a crucial role for cardiovascular and metabolic diseases in adulthood, but little is known about its impact on gonadal development and reproduction. Impaired testis development in fetal life can lead to cryptorchidism, hypospadias, impaired semen quality, and testicular cancer, disorders that may present symptoms of a testicular dysgenesis syndrome. The prevalence of these disorders appears to increase in many areas, probably due to environmental factors acting in utero. Denmark has a significantly higher incidence of testicular cancer and lower sperm quality than Finland. Methods: We conducted a population-based study of newborn boys from Denmark and Finland, in order to examine whether this geographic difference was reflected in the reproductive health of newborns. Results: Danish boys had a lower testis volume at birth, a smaller testis growth up to 18 months of age and lower serum inhibin B and FSH levels at 3 months than Finnish. Danish boys also had a higher prevalence of both cryptorchidism and hypospadias than Finnish boys. In boys with cryptorchidism and hypospadias subtle changes in hormonal levels occurred, towards increased gonadotropins and lower inhibin B in cryptorchidism. Both types of congenital malformations were more frequent in children born small for gestational age, indicative of a relationship between growth and reproductive development. Conclusions: These early postnatal findings suggest that the previously observed population differences in reproductive health between young Danish and Finnish men are of fetal origin. The differences may originate as a result of gene-environment interactions, where endocrine disrupters may also play a role.