The study had a three-fold objective: (i) to estimate the amenable mortality rates and trends at a national and state level between 2000 and 2015 in Mexico; (ii) to estimate the contribution and trends of various causes of death to overall amenable mortality; and (iii) to determine the association between health system inputs and amenable mortality for the period 2000-2015. We used a panel dataset for the period 2000-2015. The following health care inputs were used in the analysis: density of general practitioners, specialists and nurses, as well as density of hospital beds. We find that amenable mortality fell from 136 per 100,000 in 2000, to 124.1 per 100,000 in 2015 nationally, with significant heterogeneity in the trends across states. Mortality due to infectious diseases, diseases of childhood, and cardiovascular diseases decreased, while deaths due to other non-communicable diseases, such as diabetes, increased. There was a significant negative association between the density of general practitioners and specialist physicians, and amenable mortality. Our results indicate that reducing the burden of non-communicable diseases must be a health system priority. Improvements in primary health care could lead to improved disease detection and earlier diagnosis which could further reduce amenable mortality in Mexico.