Background: Medication adherence is a dynamic and complex behavioral process, which is strongly influenced by personal, social and environmental factors. Objectives: To determine the prevalence and factors affecting non-adherence to medication among HIV-infected patients. Methods and materials: Design: A cross-sectional study. Setting: Voluntary Counseling and Testing Center (VCT), Shiraz, Fars province, in the South of Iran. Patients: Among HIV-positive patients who received anti-retroviral therapy, 214 adult patients were selected through convenience sampling. Their medication adherence was checked by interview and counting the pills on visits during two months. Clinical and laboratory data were obtained from the patients' records. Results: Non-adherence and adherence groups included 30.4% (65) and 69.6% (149) of the patients, respectively. The mean age of patients was 40.80±7.77 years, and ranged from 20 to 65 years. Majority of cases (65%) were male. A significant relationship was found between non-adherence to medications and the variables of transmission method, marital status, housing status, and CD4, but there was no significant relationship with gender. Conclusion: The prevalence of medication adherence was similar to other regions with limited financial resources. To increase patient’s medication adherence, they should be exposed to motivational interventions to promote their drug consumption, social and occupational support.