Our aim was to isolate potentially important differentially expressed gene products from paired human hepatocellular carcinoma (HCC) and normal liver samples using the differential messenger RNA (mRNA) display technique. Total RNA samples were reverse transcribed with anchoring oligonucleotide primers and then amplified by the polymerase chain reaction (PCR) with additional upstream random primers. Differentially expressed complementary DNA (cDNA) products were subsequently used as probes in Northern blot analysis. One such cDNA product, present in tumor but absent in normal displays, showed identity with the adhesion molecule integrin alpha 6. In Northern blots of 16 HCC pairs, the ∼5.5 kb signal of integrin alpha 6 mRNA was overexpressed in seven tumors, with a weak signal in the normal livers. For those patients with versus without integrin alpha 6 mRNA overexpression: (1) grade III (or IV) histology was noted in seven of seven versus three of nine tumors, respectively (P = .03); (2) tumor recurrence or death (at mean follow-up of 18 months) was noted in six of seven versus three of eight patients, respectively (P = .17). Similar results were obtained using semiquantitative PCR co-amplification with glyceraldehyde 3-phosphate dehydrogenase as a control; ±50% of the tumors had stronger integrin alpha 6 bands than their paired normals. Both A and B variants of integrin alpha 6 mRNA were detectable in the tumor and normal liver samples. The B variant was more pronounced than the A variant by 8.9-fold in the tumors (n = 10) compared with threefold in the normal livers (n = 10), suggesting that the overexpression of integrin alpha 6 may be more reflective of abnormalities of B variant levels than of A variant levels. Important genes whose expression correlates with significant patient variables may be isolated by differential display; based on this small series there is a trend for integrin alpha 6 mRNA to be overexpressed in high-grade HCC and to predict a tendency toward a poorer outcome. (Hepatology 1995; 22:1447–1455).