Microarrays of cDNA provide a powerful tool for studying these complex phenomena. We used a high-density microarray of 1,400 cDNA elements to search for differences in gene expression associated with fibroblast growth factor receptor 3 (FGFR-3) K650M mutation. In this system, fluorescent probes for hybridisation were derived from two sources of human bone marrow stromal cellular mRNA (H54 and FGFR-3 K650M), which were labelled with different fluors to provide a direct and internally controlled comparison of the mRNA corresponding to each arrayed gene. We analysed the fluorescence signals representing hybridisation to each arrayed gene to determine the relative abundance in the two samples of mRNAs corresponding to each gene. There are at least 20 genes which are highly expressed in the control cells or FGFR-3 K650M mutation cells. For the gene expression level, 6 of these interesting genes were confirmed by northern blot analysis. Previously unrecognised alterations in the expression of specific genes provide leads for further investigation of the genetic basis of the dysplasia phenotype of FGFR-3 mutant cells.