A novel 1‐cM (1.8 Mb) homozygous deletion (HD) on 13q12.11 was identified in a human hepatocellular carcinoma (HCC) cell line, SK‐Hep‐1, after high‐density genetic marker scan and Southern blotting analysis. A loss of heterozygosity (LOH) analysis indicated that LOH frequency of the HD region in 48 pairs of HCC tissues was 52%. Interestingly, the occurrence of LOH in the 13q12.11 HD region is significantly associated with early‐onset HCC, inferred from Fisher's exact test (P = 0.0047) and Mann‐Whitney test (P = 0.023). Since the novel 1‐cM (1.8 Mb) HD region is gene‐rich with more than 37 predicted transcripts, we used a candidate gene approach by examining down‐regulation of known tumor suppressor genes (TSGs), including LATS2, TG737, CRYL1, and GJB2, in HCC tissues. We detected only 14% down‐regulation of the LAST2 gene that flanks the outside of the HD, in HCC tissues, by quantitative RT‐PCR assays. However, we observed significant down‐regulation of the TG737, CRYL1, and GJB2 genes located within the HD in 59, 64, and 71% of HCC tissues, respectively. Together, our results indicated that the identified 13q12.11 HD region contained at least three significant down‐regulated TSGs, and preferential LOH in early‐onset HCC patients is a putative tumor suppressor locus in HCC. © 2005 Wiley‐Liss, Inc.