Neoplastic development is a multistep process that involves the stochastic accumulation of heritable genetic alterations in proto-oncogenes, DNA repair genes, and tumor suppressor genes. Loss of heterozygosity (LOH) analysis has been used successfully to identify the genetic determinants of neoplastic development, including tumor suppressor genes, in several species and organs but not in the rat liver. We report the results of a sensitive genome-wide LOH analysis of rat hepatocellular carcinomas (HCCs). Heterozygous rats (Wistar-Furth x Fisher 344) were subjected to an Initiation-Promotion-Progression (IPP) protocol of hepatocarcinogenesis. Two weeks after initiation (by partial hepatectomy, 10 mg/kg diethylnitrosamine), the rats were placed on a diet containing 0.05% phenobarbital (PB). After 24 wk of PB promotion, the rats received either 100 or 1 50 mg/kg ethylnitrosourea. Hepatocellular tumors were resected after a total of 76wk of PB promotion. LOH analysis was completed on 26 HCCs by using 60 microsatellite markers covering all 20 rat autosomes and chromosome X. While 85% of the HCCs had one or more allelic imbalances, the average HCC had 3.3 allelic imbalances (range 0-9). A conditional hypothesis-testing method called the Hot-Cold model was used to determine the location of statistically significant elevations in the frequency of allelic imbalances. Elevated allelic imbalances were observed on chromosomes 1q, 6, 8, 11, 15, 17, and 20p. Together, these allelic imbalances suggest that the retinoblastoma and insulin-like growth factor genes as well as the resistance to chemical carcinogenesis (rcc) locus may be involved in HCC development in the rat but that LOH of the p53 gene is not. The elevated rate of allelic imbalances on chromosomes 8,11, and 17 may indicate the location of undiscovered tumor suppressor genes important to neoplastic development in rat liver. Microdissection-based LOH analysis of HCC revealed that contamination of non-neoplastic and nonhepatocellular tissue was not masking LOH in the whole-tumor analysis. There were no statistically significant differences in the frequency of allelic imbalances between HCC of any differentiation state (histological grade). To the degree that it does not reflect differences in etiological factors, the absence of allelic imbalances in chromosomal regions containing the p53 and mamose-6-phosphate/insulin-like growth factor II receptor tumor suppressor genes and the generally low frequency of allelic imbalances in these tumors, suggests that LOH and allelic imbalances play a less significant role in the molecular pathogenesis of HCC in rats than humans.