PURPOSE OF THE STUDY Although the congenital short femur is morphologically well characterized, changes at the molecular level have not been described in the literature so far. The absence of such information, along with the unknown aetiology of the defect, was the motivation for analysing angiogenesis and osteogenesis in the pseudoarthrosis (false joint) tissue in PFFD patients compared to physiological bone. The authors expected differences in gene expression, particularly in the quantity of expressed genes. MATERIAL AND METHODS A piece of bone was removed during an elective surgery procedure, placed in an RNA stabilization reagent, which prevents RNA degradation, and deep frozen. Thereafter, RNA was isolated and the profile of transcription was analysed by biochip analysis (SuperArray Bioscience Corporation). In total, it is possible to detect 113 genes of osteogenesis and angiogenesis. From the end of 2005 until the end of 2008, samples of 7 patients with PFFD and 3 physiological bone samples were examined. Several analyses were repeated to confirm the results; in total 13 chips for osteogenesis and 11 chips for angiogenesis expression were used. RESULTS Differences in the quantity and representation of the genes were noted. Some genes were considered over-expressed in PFFD tissue compared with the control sample (e.g. the gene for calcitonin receptor, collagen XII, I alpha 2, collagen II, IX, FGFR2, fibronectin, integrin) and other genes under-expressed (e.g. the gene for annexin A5, collagen XVIII alpha1, collagen I alpha1, cathepsin K, FGFR1, FGFR3, IGF2, VEGFB). CONCLUSIONS The differences in gene expression confirmed the authors' hypothesis. So far, the results cannot be generalized; this is the first step for follow-up experiments to confirm the suggested information and to integrate it with clinical findings, such as the alternative blood supply of affected extremity in some patients. Key words: proximal femoral focal deficiency, gene expression, microarray analysis, angiogenesis, osteogenesis.