Medication adherence is essential for the control of symptoms and progression of rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). The aim of the study was to investigate medication adherence in outpatients in treatment for RA and SLE in a university hospital in Brazil. This was a quantitative, cross-sectional analytical study. A total of 92 patients (55 RA patients and 37 SLE patients) were included in the study. A structured questionnaire for patients’ interview and a form for collecting data from medical records were used for data collection. Adherence to drug treatment was assessed by the Morisky scale questionnaire. Data storage and analysis were performed using Epi Info 3.5.4 and statistical analysis by Stata/SE 12.0. The Pearson’s chi-squared test and Fisher’s exact test were applied for statistical and bivariate analyses. For multivariate data analysis the Poisson regression and the Wald test were used. The prevalence of adherence to drug treatment was 16.4% in RA patients and 45.9% in SLE patients. The final model of the multivariate analysis demonstrated associations between medication adherence and the following covariates for both RA and SLE groups: duration of therapy for rheumatic disease at the institution greater than 15 years and presence of more than six chronic comorbidities. The parameter “acquisition of medication at the high-cost pharmacy” was differently associated with medication adherence by group, and for the SLE group, living outside the city of Goiânia was a protective factor associated with adherence. This study demonstrated a low prevalence of medication adherence in patients in treatment for RA and SLE treated at this institution. These findings will serve as a base for future studies to elucidate what factors may positively or negatively affect medication adherence in this population. In addition, multidisciplinary approaches are needed to enhance adherence to drug treatment in patients in treatment for rheumatic disease.