Background: The incidence of childhood diabetes is increasing in Denmark as in the rest of the world. The aim of this investigation was to study intrauterine and early childhood risk factors for insulin dependent diabetes mellitus, and to evaluate gender differences in the effect of these. Methods/material: A number of 602 diabetic cases aged 0-14 years diagnosed 1996-1999 were identified from the Danish register of childhood diabetes. A total of 1490 non-diabetic healthy children matched by gender and date of birth were randomly selected from the Danish population register. In addition a combination of national register data and questionnaire data was used. Results: High parental age, neonatal infections and pre-eclampsia were associated with type 1 diabetes in boys, whereas being preterm was associated with an increased risk in girls. An increased risk was associated with a family history of diabetes and amniocentesis, while a decreased risk was associated with increasing birth order and maternal smoking. In a multiple logistic regression analysis, the following risk factors were significantly associated with case-control status: maternal smoking (OR: 0.6(0.4-0.9)), neonatal infection in boys (OR: 5.5(1.4-21.8)), neonatal infection in girls (OR: 0.6(0.1-3.0)), amniocentesis (OR: 1.6(1.0-2.6)), pre-school siblings (OR: 0.8(0.6-1.0)), introduction of cow's milk after the age of 3 months (OR: 0.7(0.4-0.9)) and a 1st degree family member with diabetes (OR: 9.1(95 CI:5.2-16)). Conclusion: The study showed associations between several risk factors and childhood diabetes, for some risk factors the odds ratio in boys were different from the odds ratio in girls.