Endochondral bone formation is an important process in development and growth of the skeleton; still many of the mechanisms of growth cartilage remain unknown. The aim of this study was to identify genes specifically expressed in growth cartilage by constructing a subtraction cDNA library of the articular-epiphyseal cartilage complex from neonatal foal. Two hundred and eighty-four differently expressed clones, representing five novel and 37 known genes, were detected by subtraction hybridization. The tissue specificity of these genes was verified by reverse Northern analysis, and tissue distribution was determined by Northern blot analysis. Genes were classified according to predicted function. The largest functional group was the extracellular matrix, followed by transcription, signalling, cytokines and growth factors. Gremlin, Angiopoietin-like 7, and Small acidic protein have previously not been detected in growth cartilage. Based on earlier descriptions of these genes, they may represent interesting candidates in future studies of developmental orthopedic disorders.