Allelic loss of chromosome 4q is one of the most frequent genetic aberrations found in human hepatocellular carcinoma (HCC) and suggests the presence of putative tumor suppressor genes within this region. To precisely define the region containing these tumor suppressor genes for further positional cloning, we tried a detailed deletion mapping strategy in 149 HCCs by using 49 microsatellite markers covering 4q12 ≈ 25. A common region with allelic loss has been identified based on the interstitial deletions occurring within it; this region is found between D4S1534 and D4S1572 (a 17.5-cM genetic interval). When we included all cases with limited aberration regions for comparison, 2 smaller regions were derived: 1 between D4S1534 and D4S2460 (3.52 cM) and 1 between D4S2433 and D4S1572 (8.44 cM). A few candidate genes were found to be down-regulated in HCCs, but without sequence mutations. In these HCCs, 4q alleleic loss was associated with hepatitis B virus infection status and the elevation of serum alpha-fetoprotein (⩾400 ng/mL). In conclusion, the current study not only mapped a common allelic loss region on chromosome 4q, but it also revealed that its loss may be involved in hepatitis B virus–-related hepatocarcinogenesis and the elevation of serum alpha-fetoprotein. (Hepatology 2004;40:847-854).