Background: Limited efforts have been made to evaluate medication adherence among subsidized and self-paying patients. Objective: To investigate medication adherence among patients with and without medication subsidies and to identify factors that may influence patients’ adherence to medication. Setting: Government healthcare institutions in Kuala Lumpur, Selangor, and Negeri Sembilan and private healthcare institutions in Selangor and Negeri Sembilan, Malaysia. Methods: This cross-sectional study sampled patients with and without medication subsidies (self-paying patients). Only one of the patient’s medications was re-packed into Medication Event Monitoring Systems (MEMS) bottles, which were returned after four weeks. Adherence was defined as the dose regimen being executed as prescribed on 80% or more of the days. The factors that may influence patients’ adherence were modelled using binary logistic regression. Main outcome measure: Percentage of medication adherence. Results: A total of 97 patients, 50 subsidized and 47 self-paying, were included in the study. Medication adherence was observed in 50% of the subsidized patients and 63.8% of the self-paying patients (χ²=1.887, df=1, p=0.219). None of the evaluated variables had a significant influence on patients’ medication adherence, with the exception of attending drug counselling. Patients who attended drug counselling were found to be 3.3 times more likely to adhere to medication than those who did not (adjusted odds ratio of 3.29, 95% CI was 1.42 to7.62, p = 0.006). Conclusion: There is no significant difference in terms of medication adherence between subsidized and self-paying patients. Future studies may wish to consider evaluating modifiable risk factors in the examination of non-adherence among subsidized and self-paying patients in Malaysia.