OBJECTIVES To evaluate doctors’ adherence to Malaysian Clinical Practice Guideline (CPG) 2009 in the management of diabetes mellitus with co-morbidities in Malaysia.  METHODS Cross-sectional study was done at a tertiary-care hospital in Malaysia. Total 51 physicians and 1020 patients’ prescriptions written by same physicians (20 prescriptions per physician) were analyzed. All patients had diabetes mellitus with co-morbidities. Depending on the recommendations of CPG 2009, the prescriptions were clustered as adherent and non-adherent prescriptions. All obtained data were analyzed using descriptive and inferential statistics. RESULTS A statistically significant negative association (Ф= 0.094, p-value=0.003) was observed between diabetes mellitus control and co-morbidities. CPG adherent had statistically weak negative association (Ф= - 0.081, p-value=0.010) with patients having co-morbidities (41.6%). No statistically significant association was observed between CPG adherence and any other co-morbidity. Majority of the patients received guidelines-compliant pharmacotherapy. The overall good level of physician adherence with CPG 2009 was observed in the management of diabetes mellitus with co-morbidities. CONCLUSIONS The study explored several features of prescription pattern of the physicians involved in the management of diabetes mellitus with co-morbidities and recognized the need for improvement in their prescription pattern for treating the diabetes mellitus.