Protein-protein interactions play a central role within numerous processes in the cell. The relevance of the processes in which this type of interactions are implicated make them responsible for many pathological situations. In the last decade protein-protein interfaces have shown their potential as new drug targets, and combinatorial chemistry has been defined as a useful tool in this line. This review gives a global vision of the actual situation of combinatorial chemistry, highlighting its applicability to high-throughput drug discovery and giving some crucial examples of its contribution to find modulators of protein-protein interactions.