Many people use cannabis for medical reasons despite limited evidence of therapeutic benefit and potential risks. Little is known about medical practitioners’ documentation of medical cannabis use or clinical characteristics of patients with documented medical cannabis use. To estimate the prevalence of past-year medical cannabis use documented in electronic health records (EHRs) and to describe patients with EHR-documented medical cannabis use, EHR-documented cannabis use without evidence of medical use (other cannabis use), and no EHR-documented cannabis use. This cross-sectional study assessed adult primary care patients who completed a cannabis screen during a visit between November 1, 2017, and October 31, 2018, at a large health system that conducts routine cannabis screening in a US state with legal medical and recreational cannabis use. Three mutually exclusive categories of EHR-documented cannabis use (medical, other, and no use) based on practitioner documentation of medical cannabis use in the EHR and patient report of past-year cannabis use at screening. Health conditions for which cannabis use has potential benefits or risks were defined based on National Academies of Sciences, Engineering, and Medicine’s review. The adjusted prevalence of conditions diagnosed in the prior year were estimated across 3 categories of EHR-documented cannabis use with logistic regression. A total of 185 565 patients (mean [SD] age, 52.0 [18.1] years; 59% female, 73% White, 94% non-Hispanic, and 61% commercially insured) were screened for cannabis use in a primary care visit during the study period. Among these patients, 3551 (2%) had EHR-documented medical cannabis use, 36 599 (20%) had EHR-documented other cannabis use, and 145 415 (78%) had no documented cannabis use. Patients with medical cannabis use had a higher prevalence of health conditions for which cannabis has potential benefits (49.8%; 95% CI, 48.3%-51.3%) compared with patients with other cannabis use (39.9%; 95% CI, 39.4%-40.3%) or no cannabis use (40.0%; 95% CI, 39.8%-40.2%). In addition, patients with medical cannabis use had a higher prevalence of health conditions for which cannabis has potential risks (60.7%; 95% CI, 59.0%-62.3%) compared with patients with other cannabis use (50.5%; 95% CI, 50.0%-51.0%) or no cannabis use (42.7%; 95% CI, 42.4%-42.9%). In this cross-sectional study, primary care patients with documented medical cannabis use had a high prevalence of health conditions for which cannabis use has potential benefits, yet a higher prevalence of conditions with potential risks from cannabis use. These findings suggest that practitioners should be prepared to discuss potential risks and benefits of cannabis use with patients.