Objective To gain a better understanding of genetic changes in Cantonese nasopharyngeal carcinoma (NPC). Methods Comparative genomic hybridization (CGH) was performed on 17 primary nasopharyngeal carcinomas.Results A novel copy number gain an chromosome 4q and loss of chromosome lp were found at a high frequency (>50%). Conclusions Current analysis revealed a comprehensive profile of the chromosomal regions showing gain of chromosomes 4q, 12q, and lq as well as loss of chromosomes 1p, 3p, 11q, 14q, 15q, 13q, Xq, 9q, 10p, 10q, and 16q. Frequently altered loci may encode oncogenes or tumor suppressor genes involved in the development of primary NPC.