Identification of the basic genetic changes in human hepatocellular carcinoma (HCC) is very important for the understanding of this cancer. In this study, genomic DNA from 29 pairs of HCC and corresponding non-tumour tissues infected with hepatitis B virus (HBV) was prepared. Five CA-repeated microsatellite markers, including D8S277, D3S1029, D5S409, D2S123, and TP53, were used to analyse microsatellite alterations and their subtypes in these patients by polymerase chain reaction (PCR) amplification and denatured polyacrylamide gel electrophoresis. Microsatellite alterations were found in 15 of the 29 HCC patients (51.72%), implying that microsatellites are unstable in genomic DNA of HBV-infected HCC. It was found that frequency of microsatellite alterations in these HCC patients was not associated with patients' age, sex, status of tumour differentiation, and tumour size. Frequency of microsatellite alterations in HCC patients with cirrhosis tended to be less than that in patients without cirrhosis, but Fisher's exact test, 2-tailed, showed that this difference was not significant. Significantly more microsatellite alterations in serum alpha-fetoprotein (AFP)-positive cases were observed than those in serum AFP-negative ones, implying that the elevation of AFP in HBV-infected HCC may be associated with microsatellite stability.