Hepatocellular carcinoma (HCC) arising in cirrhosis is frequently multifocal. Whether HCC develops monoclonally or multiclonally is an unresolved question. Of the multiple tumour nodules which often develop in cirrhotic, it has not been established whether the smaller lesions represent intrahepatic metastases or de novo cancers. The degree of genomic heterogeneity was therefore assessed, and the clonal evolution was studied in synchronous HCCs in cirrhosis from patients undergoing elective orthotopic liver transplantation. All samples studied were negative on p53 immunohistochemistry, and no mutation in exons 5-9 of the p53 gene was found by performing polymerase chain reaction and direct DNA sequencing analysis. Using arbitrarily primed-polymerase chain reaction (AP-PCR) technique, reproducible and interpretable fingerprinting patterns of amplified genomic DNA isolated from microdissected paraffin-embedded tissues were generated. The fingerprints were highly polymorphic amongst HCCs and regenerative nodules. Clonal evolution was found to occur in HCCs more than 6 mm in diameter which consistently contain multiple clones. In addition, the genomic fingerprint patterns of the extra-hepatic metastatic lesions were polymorphic compared to those of the corresponding primary HCCs. By contrast, DNA fingerprints of multiple areas of primary fibrolamellar carcinomas (FLCs) and all their metastatic lesions were identical. The advent of laser capture microdissection (LCM) technology allowed analysis of selected cell groups within a single tumour much more rapid and simple to apply. The control of neovascularisation in tumours, particularly in HCCs, depends on a net balance of positive and negative angiogenic factors. Transfection of thrombospondin-1, an important negative factor, into Sk-Hep-1 cells was associated with decreased thymidine incorporation in vitro and reduced primary tumour growth in vivo. Antiangiogenic therapy after removal of a dominant HCC might be a useful treatment to suppress the growth of residual or synchronous tumours.