Our previous study of gene alterations in 29 hepatocellular carcinoma (HCC) using AP-PCR amplified with 59 different 10-mer arbitrary primers and gene cloning, indicated DNA alterations by DNA fingerprints from 34 primers. Among these, the altered DNA fragment from primer U-8 predominated (62%). The aim of this report is to identify the gene alterations on chromosomal banding and gene expression in these patients, including the association of these alterations with patient demographic data. Seven different sequences, mapped to chromosomes 5q33.3, 7q31.33, 7q34, 9p24.3, 10q25.3, 13q31.3, and 16p11.2, were identified by gene cloning and nucleotide sequencing. Novel PNLIPRP3 gene over-expression and DOCK8 gene under-expression were observed in 41% and 44% of these patients, respectively, which point to an association of these genes and the development of HCC. Likewise, allelic loss on chromosome 10q25.3 was associated with shorter survival among HCC patients (P=0.03); this indicated that allelic loss on chromosome 10q25.3 may serve as a prognostic marker in patients with HCC.