Research confirms that maternal ethanol (EtOH) exposure can induce physical and mental disorders in offspring, yet the effect of paternal ethanol exposure on offspring is unclear. Methylation alterations in imprinted genes may be related to the well-documented teratogenic effects of ethanol. Here, we report that ethanol (0, 1.1, 3.3 g/kg) was administered intragastrically to male mice and a behavioral study was performed on their F1 generation. Data show that F1 mice with fathers exposed to the highest dose of ethanol had delayed cognitive performance and increased anxiety and depression. A specific circling behavior was observed in the offspring of the paternally ethanol-exposed group. The degree of methylation and mRNA expression of H19, Peg3, Ndn and Snrpn were assessed in paternal sperm and in the cerebral cortices of each offspring. It did affect methylation in paternal sperm (H19 and Peg3) and in the offspring's cerebral cortices (CpG7 and CpG11 in Peg3 and Snrpn), but the level of mRNA expression has not changed. In the circling mice, the highest ethanol exposure increase in methylation (CpG 1, 2, 7 and 11) and decreases in mRNA of Peg3.Thus, chronic paternal ethanol exposure can affect the methylation of imprinted genes in sire sperm that may be passed on to offspring, giving rise to mental deficits.