Chromosomal loss of heterozigosity (LOH) is a common mechanism for the inactivation of tumor suppressor genes in human epithelial cancers. Hybridization of genomic DNA to single nucleotide polymorphism (SNP) array is an efficient method to detect genome wide cancer LOH. Here we report preliminary results of the analysis of DNA samples obtained from clear renal cell carcinoma (cRCC) patients by Affymetrix microarray technology. DNA samples from dissected tumor tissues and the corresponding autologous blood were used. Human Mapping 10K GeneChips® that allow the simultaneous analysis of 11.560 SNPs distributed over all human chromosomes were used following manufacter’s protocol. Affymetrix genotyping software (GDAS) was used for SNP calling and allelic losses were determined integrating various statistical tools. SNPs annotation was derived from different public databases (SNPper, IGB,UCSC Genome Browser). To determine chromosomal alterations we considered the chromosome distribution either of LOH calls (AB in blood, A or B in tumor) and NoCall data (AB, A or B in blood, N in tumor).Using SNP array we were able to identify a set of genomic LOH regions including 3p26-p24 and 3p14 cytobands. Our results are in agreement with already published papers on cRCC LOH. However in order to characterize with more accuracy chromosomal allelic instability using SNP markers, further analysis by Human Mapping 50K GeneChips® is in progress.This work was supported by grants from the Italian Ministry of University and Research (RBNE01TZZ8,RBNE01HCFK,COFIN2004) and from CISI,University of Milan, Italy.