The S100 protein family is a highly conserved group of Ca²⁺‐binding proteins that belong to the EF‐hand type and are considered potential drug targets. In the present study we focused our attention on two members of the family: S100A13 and S100B; the former is involved in the nonclassical protein release of two proangiogenic polypeptides FGF‐1 and IL‐1α that are involved in inflammatory processes, whereas S100B is known to interact with the C‐terminal domain of the intracellular tumor suppressor p53 and promote cancer development. We screened, using waterLOGSY NMR experiments, 430 molecules of a generic fragment library and we identified different hits for each protein. The subset of fragments interacting with S100B has very few members in common with the subset interacting with S100A13. From the ¹⁵N‐HSQC NMR spectra of the proteins in the presence of those hits the chemical shift differences Δδ(HN) were calculated, and the main regions of surface interaction were identified. A relatively large variety of interaction regions for various ligands were identified for the two proteins, including known or suggested protein–protein interaction sites.