More than 70 missense mutations have been identified in the human melanocortin 4 receptor (MC4R) and many of them have been associated with obesity. In a number of cases the causal link between mutations in MC4R and obesity is controversially discussed. Here, we mined evolution as an additional source of structural information that may help to evaluate the functional relevance of naturally occurring variations in MC4R. The sequence information of more than 60 MC4R orthologs enabled us to identify residues that are important for maintaining receptor function. More than 90% of all inactivating mutations found in obese patients where located at amino acid positions which are highly conserved during 450 million years of MC4R evolution in vertebrates. However, for a reasonable number of MC4R variants we found no correlation between structural conservation of the mutated position and the reported functional consequence. By reevaluating selected mutations in the MC4R we demonstrate the usefulness of combining functional and evolutionary approaches.