Comorbid medical conditions may influence treatment and contribute to poor outcomes in early RA. We aimed to assess the association of baseline comorbidity with outcomes in early inflammatory arthritis using data from the Canadian Early Arthritis Cohort. Patients (n = 2090) with early inflammatory arthritis (symptom duration of < 1 year) reported comorbid medical conditions at baseline. Functional status (HAQ), detailed clinical assessments and treatment were assessed. Treatment is not protocolized but participating rheumatologists aim for remission. The influence of comorbidity on clinical outcomes was determined using multivariate models. At least one comorbid condition was reported by 76% of patients. Patients with comorbidity were older (mean age 56 vs 44 years, P < 0.0001) and had worse baseline function [median (interquartile range, IQR) HAQ score (0.88 (1) vs 0.75(1), P < 0.0001] compared with those without comorbidity even after controlling for age, sex and symptom duration. At 1 year, patients with baseline comorbidity were less likely to achieve remission (odds ratio, OR = 0.67; 95% CI: 0.51, 0.88, P = 0.004) and had higher HAQ [median (IQR) 0.25 (1) vs 0 (0), P < 0.0001] and pain scores [median (IQR) 2.85 (4) (out of 10) vs 1 (4), P < 0.0001] than patients without comorbidity after adjusting for age, sex, symptom duration, baseline disease activity and arthritis treatment. Comorbidity is common in early inflammatory arthritis and associated with higher disease activity, worse functional status and greater pain scores during the first year of follow-up. While the mechanisms for this association require investigation, addressing comorbidity may improve clinical outcomes in early RA.