<p>Sex-specific differences in liver gene expression have previously been reported in humans and rodents. Clinically, female-to-male liver transplants are known to be associated with adverse post-transplantation outcomes. However, the underlying molecular mechanisms remain largely unknown. Sex-specific gene expression differences may be involved in the post-transplantation outcomes. Here, we analyse sex-specific differences in liver gene expression of Lewis rats on a genome-wide scale. In total, 543 genes exhibited a differential gene expression between male (<i>n</i> = 4) and female (<i>n</i> = 4) rats, with the largest difference found for the transcript ENSRNOG00000009273.7 (log₂FC = 10.69, <i>p</i> &lt; 2.2*10^− 308). Genes downregulated (<i>n</i> = 272) in males were enriched for cholesterol homeostasis and late oestrogen response. We further analysed inter- and intra-sex gene expression differences in three individual liver sections to evaluate liver heterogeneity. Although several genes exhibited a sex-specific expression in all three liver sections (<i>n</i> = 240), distinct expression patterns within each individual section were determined. Variations between sections were even evident within the same sex with male liver sections revealing more differentially expressed genes (male <i>n</i> = 40, female <i>n</i> = 11). Consequently, studies investigating liver-specific gene expressions should consider this intrahepatic heterogeneity to avoid introducing potential biases. Subsequent studies ought to explore gene expression differences between the sexes pre- and post-transplantation, particularly regarding a female-to-male transplants.</p>