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Introduction Diabetes and its complications are a major cause of morbidity and mortality in the Philippines. The prevalence of diabetes in the Philippines has increased from 3.4million in 2010 to 3.7million in 2017. The government has formulated strategies to control this increase, for example, through its non-communicable disease prevention and control plan. However, there is scarce research on the financial burden of diabetes. Filling this gap may further help policymakers to make informed decisions while developing and implementing resource planning for relevant interventions. The primary objective of the current study is to estimate the direct medical costs associated with type 2 diabetes mellitus (T2DM). Methods and analysis This is a 1-year retrospective cohort study of patients with T2DM in 2016. Data will be collected from: (1) hospital databases from public institutions to estimate the cost of diabetes treatment and (2) physician interviews to estimate the cost of management of diabetes in outpatient care. We will perform descriptive and comparative analyses on direct medical costs and healthcare resource utilisation, stratified by the presence of diabetes-associated complications. Ethics and dissemination Research ethics board approval has been obtained from the Department of Health Single Joint Research Ethics Board and Cardinal Santos Medical Center Research Ethics Review Committee. Findings from the study will be reported in peer-reviewed scientific journals and local researcher meetings. [ABSTRACT FROM AUTHOR]