Introduction Patients with IgA vasculitis (IgAV) may require aggressive treatment and are prone to disease relapses, and IgA deposition in tissues can persist. We investigated whether these factors predispose to long-term morbidity in children with IgAV. Methods Observational cohort study comparing rates for comorbidity development by Charlson comorbidity index (CCI) and rates for hospitalization, procedures, and emergency department (ED) visits over a 20-year period for IgAV patients <20 years (n = 494) and matched hospital-based controls (n = 1385). Odds (OR) for events and rate ratios (RR) for event rates per 1000 person-years were derived from maximum likelihood estimates. Results Patient survival (99.1 vs. 99.7%,p = 0.6) and overall comorbidity accrual CCI (0.21 vs. 0.23,p = 0.7) were similar for IgAV patients and hospital-based controls after 20 years. IgAV patients did not develop other rheumatic diseases, but more often were diagnosed with peptic ulcer and end-stage renal failure. Hospitalization rates were three times higher for IgAV patients (RR 3.41 CI 3.04-3.82) in the first year following diagnosis, while ED attendance rates were higher in subsequent years (RR 1.29; 1.02-1.04;p <0.01) for IgAV patients. Conclusions Childhood IgAV patients have good long-term prognosis despite the occurrence of end-stage renal failure and compared to hospital-based controls are at not at increased risk for other comorbidity or rheumatic disease.