Furan, a widely used industrial compound, has been found in a number of heated food items. Furan is carcinogenic to rats and mice, but the mechanism behind its carcinogenic effect is still not well understood. In this study, we tested the hypothesis that alteration of gene expression relating to cell cycle, apoptosis, DNA damage and of epigenetic modifications including miRNA and DNA methylation may contribute to rodent carcinogenicity of furan. Using quantitative PCR arrays specific to cell cycle-, apoptosis- and DNA damage-related genes, we found that three months furan treatment at 30mg/kg (5 daily doses per week) induced extensive mRNA expression changes (largely up-regulation) in male Sprague Dawley rat liver, and the gene expression changes did not fully recover after a one month withdrawal of furan. We also found 18 miRNAs were up-regulated and 12 were down-regulated by PCR arrays. Many of these deregulated miRNAs were also found to have similar changes in furan-induced tumour samples. Both hyper- and hypo-methylation of specific gene promoter regions were identified and validated in the 3-month samples and tumour samples by microarray and COBRA (combined bisulfite restriction analysis). No global DNA methylation change was found in the 3 month treatment groups by LC-MS/MS, while furan-induced tumour samples showed global hypomethylation compared to non-tumour tissues. In conclusion, three months furan treatment at a carcinogenic dose resulted in irreversible gene expression changes, miRNA modulation and DNA methylation alteration in combination with a DNA-damage response, which suggests that non-genotoxic mechanisms are important for furan carcinogenicity.