Clinical practice guidelines recommend that clinicians implement the 5As (Ask, Advise, Assess, Assist, and Arrange) for smoking cessation at every clinical encounter. We sought to examine the prevalence of patient- and clinician-reported 5As in two primary care and one HIV care clinics in San Francisco, California between August 2013 and March 2014 (n = 462 patients and n = 61 clinicians). We used multivariable logistic regression analysis to identify factors associated with receipt of the 5As, adjusting for patient demographics, patient insurance, clinic site, patient tobacco use, and patient comorbidities. The patient-reported prevalence of 5As receipt was as follows: Ask, 49.9%; Advise, 47.2%; Assess, 40.6%; any Assist, 44.9%; and Arrange, 22.4%. In multivariable analysis, receipt of Advise, Assess, and Assist were associated with older patient age. Whereas patients with HIV had a lower odds of reporting being advised (AOR 0.5, 95% CI 0.3-0.8) or assessed for readiness to quit (AOR 0.6, 95% CI 0.4-0.9), patients with pulmonary diseases had higher odds of reporting being assisted (AOR 1.6, 95% 1.0-2.6) than patients without these diagnoses. Although the majority of clinicians reported asking (91.8%), advising (91.8%), and assessing (93.4%) tobacco use 'most of the time' or 'always' during a clinical encounter, fewer reported assisting (65.7%) or arranging (19.7%) follow-up. Only half of patients reported being screened for tobacco use and fewer reported receipt of the other 5As, with significant disparities in receipt of the 5As among patients with HIV. Our findings confirm the need for interventions to increase clinician-delivered cessation treatment in primary and HIV care.