In most countries, surprisingly little is known on how national healthcare spending is distributed across diseases. Single-disease cost-of-illness studies cover only a few of the diseases affecting a population and in some cases lead to untenably large estimates. The objective of this study was to decompose healthcare spending in 2011, according to Swiss National Health Accounts, into 21 collectively exhaustive and mutually exclusive major disease categories. Diseases were classified following the Global Burden of Disease Study. We first assigned the expenditures directly mapping from National Health Accounts to the 21 diseases. The remaining expenditures were assigned based on diagnostic codes and clues contained in a variety of microdata sources. Expenditures were dominated by non-communicable diseases with a share of 79.4%. Cardiovascular diseases stood out with 15.6% of total spending, followed by musculoskeletal disorders (13.4%), and mental and substance use disorders (10.6%). Neoplasms (6.0% of the total) ranked only sixth, although they are the leading cause of premature death in Switzerland. These results may be useful for the design of health policies, as they illustrate how healthcare spending is influenced by the epidemiological transition and increasing life expectancy. They also provide a plausibility check for single cost-of-illness studies. Our study may serve as a starting point for further research on the drivers of the constant growth of healthcare spending.