One of the major challenges in cancer research is to generate molecular profiles of tumours and establish correlations between genetic changes and clinical parameters by screening technologies. The identification of tumour-specific gene targets has potential diagnostic and therapeutic implications. Metaphase comparative genomic hybridisation has been used to detect relative DNA-sequence copy number gains (including high-level amplifications of chromosomal regions) and copy number losses in human neoplasms. In the past, metaphase comparative genomic hybridisation has been shown to be a powerful genome-wide screening method and this has considerably advanced our understanding of renal cancer biology. Novel molecular technologies, including array-based comparative genomic hybridisation, fluorescence in situ hybridisation (FISH), cDNA and tissue microarrays will serve to facilitate further characterisation of candidate genes residing in chromosomal regions defined by metaphase comparative genomic hybridisation. This review concentrates on the application of metaphase comparative genomic hybridisation in the area of renal cancer research and summarises data obtained from comparative genomic hybridisation studies.