The active site of cyclooxygenase was modeled by complementary receptor-cavity mapping procedure using 3D structures of the non-steroidal antiinflammatory drugs (NSAIDs). A total of 50 NSAIDs were chosen as data ligands which compete the same site on the enzyme. Partial atomic charges were estimated, and the energetic differences for various conformations were calculated so as to meet the need for a most efficient overlapping of the probably-equivalent functional groups of the ligand molecules. The structure activity relationships of the NSAIDs, if available, were fully considered throughout the modeling. The overall shape of the model obtained is similar to a boot-without-bottom. Most of inner surface of the cavity appeared as hydrophobic: two polar counterparts except the carboxyl-binding position were found. By this model, some clear explanations could be given on the experimental observations which were not satisfiably understood yet.