Alopecia areata (AA) is associated with an increased burden of autoimmune and inflammatory disease and mental health conditions that may have a negative impact on quality of life. However, the exact burden of comorbidities on US patients with AA and the clinical subtypes alopecia totalis (AT) and alopecia universalis (AU) compared with those without AA is not well understood. This retrospective cohort study aimed to assess the incidence rates and prevalence of AA and its clinical subtypes and examine the autoimmune and inflammatory disease and mental health condition diagnosis burden in US patients with AA and a matched cohort without AA. The Optum Clinformatics Data Mart database was used to select patients aged ≥12 years enrolled between October 1, 2016, and September 30, 2020, who had two or more AA diagnosis codes for the AA cohort. Three patients without AA were age-, sex-, and race-matched to each patient with AA. Autoimmune and inflammatory diseases and mental health conditions were evaluated at baseline and up to 2 years after the index date. In total, 8784 patients with AA (599 with AT/AU) and 26 352 matched patients without AA were included. The incidence rate of AA was 17.5 per 100 000 person-years (PY; AT/AU: 1.1 per 100 000 PY; non-AT/AU: 16.3 per 100 000 PY), and the prevalence was 54.9 per 100 000 persons (AT/AU: 3.8; non-AT/AU: 51.2). Patients with AA had a higher prevalence of autoimmune and inflammatory diseases than the matched non-AA cohort, including allergic rhinitis (24.0% vs 14.5%), asthma (12.8% vs 8.8%), atopic dermatitis (8.3% vs 1.8%), and psoriasis (5.0% vs. 1.6%). The proportions of anxiety (30.7% vs 21.6%) and major depressive disorder (17.5% vs 14.0%) were higher in patients with AA than those without AA. Patients with AT/AU generally had a greater prevalence of autoimmune and inflammatory disease and mental health conditions than patients with non-AT/AU AA.