Several prospective studies have shown an association between cow’s milk consumption and the risk of islet autoimmunity and/or type 1 diabetes. We wanted to study whether processing of milk plays a role. A population-based birth cohort of 6081 children with HLA-DQB1-conferred risk to type 1 diabetes was followed until the age of 15 years. We included 5545 children in the analyses. Food records were completed at the ages of 3 and 6 months and 1, 2, 3, 4, and 6 years and diabetes-associated autoantibodies were measured at 3–12 month intervals. For milk products in the food composition database we used conventional and processing-based classifications. We analysed the data using a joint model for longitudinal and time-to-event data. By the age of 6 years, islet autoimmunity developed in 246 children. Consumption of all cow’s milk products together [energy-adjusted hazard ratio (95% confidence interval) 1.06 (1.02, 1.11), P=0.003], non-fermented milk products [1.06 (1.01, 1.10), P=0.011], and fermented milk products [1.35 (1.10, 1.67), P=0.005] were associated with an increased risk of islet autoimmunity. The early milk consumption was not associated with the risk beyond 6 years. We observed no clear differences based on milk homogenisation and heat treatment. Our results are consistent with the previous studies, which indicate that high milk consumption may cause islet autoimmunity in children at increased genetic risk. The study did not identify any specific type of milk processing that would clearly stand out as a sole risk factor apart from other milk products.