Genomic instability as reflected by microsatellite alterations in specific target regions is an important characteristic of oral squamous cell carcinoma (OSCC). Microsatellite instability (MSI) and loss of heterozygosity (LOH) on chromosome 9 has been reported as an early event in oral cancers, primarily from patients in the USA and UK. Hence, we examined 77 primary oral cancer tissues and corresponding peripheral blood cell (PBC) DNA from Indian oral cancer patients for LOH and MSI, using a panel of 11 microsatellite markers spanning chromosome 9 on p and q arms. The patients were long-time (minimum 10 years) tobacco chewers. The matched DNA samples were amplified by polymerase chain reaction, resolved on a denaturing polyacrylamide gel and visualized by silver staining. An overall of 62% (48/77 cases) of the patients demonstrated microsatellite alterations including 27% MSI and 52% LOH, although at individual loci MSI was observed in 3-8% patients and LOH in the informative cases ranged from 4 to 41%. A majority of the alterations occurred on the p arm at 9p21-23, with 85% (41/48 cases) genetic alterations concentrated between markers D9S157 and D9S161. Multiple alterations were seen in 56% (27/48) of the affected cases with 17 patients showing microsatellite alterations in three to eight loci. Our data show the incidence of genetic alterations primarily in the chromosomal region 9p21-23, and may be indicative of involvement of p16 (CDKN2) tumor suppressor gene on chromosome 9p21, in a subset of chewing tobacco-induced oral cancers.