Mental illness has been previously linked with autoimmune diseases, yet the associations between parental mental illness and offspring's risk of autoimmune diseases is largely unknown. We conducted a population-based cohort study of 2,192,490 Swedish children born between 1991 and 2011 and their parents to determine the associations between parental mental illness and risk of autoimmune diseases among the offspring. Time-dependent diagnoses of parental mental illness (psychosis, alcohol/drug misuse, depression, anxiety, eating disorders, personality disorders, attention deficit hyperactivity disorder, autism spectrum disorder) and offspring autoimmune diseases (type 1 diabetes (T1D), juvenile idiopathic arthritis (JIA), systemic lupus erythematosus, psoriasis, multiple sclerosis, inflammatory bowel disease (IBD), coeliac disease) were identified from inpatient/outpatient healthcare visits. Associations were measured by hazard ratios (HRs) adjusted for potential confounders. Overall, parental mental illness was associated with a small increase in risk of offspring's autoimmune diseases (HR 1.05, 95% CI 1.02-1.08). However, parental common mental disorder (anxiety/depression) was associated with higher risk of JIA, psoriasis, and T1D (HR T1D 1.11, 95% CI 1.01-1.22), while maternal psychosis with reduced risk of coeliac disease (HR 0.68, 95% CI 0.49-0.95) and paternal alcohol/drug misuse with reduced risk of IBD (HR 0.80, 95% CI 0.64-0.99). Maternal eating disorders were associated with a markedly increased risk for T1D (HR 1.41, 95% CI 1.05-1.89). Further studies are needed to confirm these findings and to understand underlying mechanisms. There is a need for greater clinical awareness about potential risk of JIA, psoriasis, and T1D among children of parents with common psychiatric morbidity.