The VHL tumor suppressor gene (TSG) at 3p25-26 is strongly implicated in the pathogenesis of clear cell renal cell carcinoma (cRCC). In addition, 3p14.2 and 3p21 are suspected of harboring additional TSGs in cRCC, with FHIT being a candidate TSG at 3p14.2. We examined 87 microdissected, histologically well-defined cRCCs classified according to tumor-node-metastasis (TNM) stage (stage 1, 23 cases; stage 2, 14 cases; stage 3, 24 cases; stage 4, 26 cases) and Fuhrman grade (grade 1, 24 cases; grade 2, 19 cases; grade 3, 19 cases; grade 4, 8 cases; sarcomatoid cRCC, 17 cases) for loss of heterozygosity (LOH) at 3p14.2 and 3p25-26 using a series of precisely mapped microsatellite probes. We found that LOH at 3p14.2 exceeded LOH at 3p25-26 in frequency (69% versus 48.3%; P < 0.03) and was highly localized to markers within the FHIT gene locus (D3S1300 and D3S4260), with the majority of chromosomal breakpoints also mapping to this region. In addition, 3p14.2 LOH (P < 0.03), but not 3p25-26 LOH (P = nonsignificant), was associated with lower tumor grades (grades 1-3). These findings suggest that 3p14.2 genomic deletions may be among the earliest events in cRCC pathogenesis, preceding genomic deletions at the VHL locus. FHIT, or an as yet undiscovered TSG mapping to the D3S4103-D3S4260 interval, could be the molecular target of the 3p14.2 deletions.