Subungual exostosis is a benign bone- and cartilage-producing tumor occurring in the hands and feet of children and young adults. The recent identification of a recurrent chromosomal translocation t(X;6)(q24-q26;q15-21) in short-term-cultured tumor cells strongly suggests that subungual exostosis is a neoplastic lesion caused by rearrangement of genes in the two breakpoints. To identify the genes that are critical for neoplastic transformation, we have studied five subungual exostoses by interphase or metaphase FISH. The results of these analyses demonstrated a clustering of the breakpoints to the regions harboring the collagen genes COL12A1 and COL4A5 in chromosome bands 6q13-14 and Xq22, respectively. Furthermore, in all but one case, these two genes were shown to colocalize on the derivative chromosomes X and 6, strongly suggesting that at least one of them is consistently involved in the formation of a chimeric fusion gene or in the exchange of regulatory sequences. Because collagen molecules are important for tissue remodeling during physiologic growth and differentiation, both COL12A1 and COL4A5 constitute good candidate target genes in the pathogenesis of subungual exostosis. Further investigations on the transcript level are required to elucidate the functional outcome of the t(X;6) translocation in subungual exostoses.