Abstract Aims Autoimmune systemic inflammatory diseases (SIDs) are associated with an increased risk of cardiovascular (CV) disease, particularly myocardial infarction (MI). However, there are limited data on the prevalence and effects of SID among adults who experience an MI at a young age. We sought to determine the prevalence and prognostic implications of SID among adults who experienced an MI at a young age. Methods and results The YOUNG-MI registry is a retrospective cohort study from two large academic centres, which includes patients who experienced a first MI at 50 years of age or younger. SID was ascertained through physician review of the electronic medical record (EMR). Incidence of death was ascertained through the EMR and national databases. The cohort consisted of 2097 individuals, with 53 (2.5%) possessing a diagnosis of SID. Patients with SID were more likely to be female (36% vs. 19%, P = 0.004) and have hypertension (62% vs. 46%, P = 0.025). Over a median follow-up of 11.2 years, patients with SID experienced an higher risk of all-cause mortality compared with either the full cohort of non-SID patients [hazard ratio (HR) = 1.95, 95% confidence interval (CI) (1.07–3.57), P = 0.030], or a matched cohort based on age, gender, and CV risk factors [HR = 2.68, 95% CI (1.18–6.07), P = 0.018]. Conclusions Among patients who experienced a first MI at a young age, 2.5% had evidence of SID, and these individuals had higher rates of long-term all-cause mortality. Our findings suggest that the presence of SID is associated with worse long-term survival after premature MI.