Mutations in the cartilage oligomeric matrix protein (COMP) gene cause both pseudoachondroplasia (PSACH) and multiple epiphyseal dysplasia (MED). Most mutations in COMP are located in the region encoding type 3 thrombospondin like domain (TSP3D). We report two Japanese boys with PSACH who had different novel in-frame deletions in TSP3D. The result recapitulates previous reports in that the in-frame deletions in TSP3D preferentially caused PSACH rather than MED.