Background: Chronic diseases (CD) are a public health emergency in Mexico. Despite concern regarding the financial burden of CDs in the country, economic studies have focused only on diabetes, hypertension, and cancer. Furthermore, these estimated financial burdens were based on hypothetical epidemiology models or ideal healthcare scenarios. The present study estimates the annual expenditure per patient and the financial burden for the nine most prevalent CDs, excluding cancer, for each of the two largest public health providers in the country: the Ministry of Health (MoH) and the Mexican Institute of Social Security (IMSS). Methods: Using the Mexican National Health and Nutrition Survey 2012 (ENSANUT) as the main source of data, health services consumption related to CDs was obtained from patient reports. Unit costs for each provided health service (e.g. consultation, drugs, hospitalization) were obtained from official reports. Prevalence data was obtained from the published literature. Annual expenditure due to health services consumption was calculated by multiplying the quantity of services consumed by the unit cost of each health service. Results: The most expensive CD in both health institutions was chronic kidney disease (CKD), with an annual unit cost for MoH per patient of US$ 8,966 while for IMSS the expenditure was US$ 9,091. Four CDs (CKD, arterial hypertension, type 2 diabetes, and chronic ischemic heart disease) accounted for 88% of the total CDs financial burden (US$ 1.42 billion) in MoH and 85% (US$ 3.96 billion) in IMSS. The financial burden of the nine CDs analyzed represents 8% and 25% of the total annual MoH and IMSS health expenditure, respectively. Conclusions/Significance: The financial burden from the nine most prevalent CDs, excluding cancer, is already high in Mexico. This finding by itself argues for the need to improve health promotion and disease detection, diagnosis, and treatment to ensure CD primary and secondary prevention. If the status quo remains, the financial burden could be higher.