Aims: To investigate the effect of acute in vivo administration of ethanol on acetylation or methylation of histone H3 at lysine9 in different tissues in rat. Methods: Ethanol was injected into the stomach of Sprague–Dawley rats (8-weeks-old) using blunt tipped needle. The rats were divided into three groups based on ethanol exposure times (1, 3, and 12 h). Each group was compared with water-injected control group. The tissues from 14 different organs were removed. We essentially used similar type of protocol, tissue homogenization method, and sucrose density gradient centrifugation for isolation of nuclei with only minor modifications for some organs. Histone was isolated from the nuclei using acid extraction method. Acetylation of histone H3 at lysine9 (Ac-H3-lys9) and methylation of histone H3 at lysine9 (Me-H3-lys9) were analysed by western blotting. Results: Effect of ethanol on Ac-H3-lys9 was investigated in 11 out of 14 rat tissues. In liver, we observed an increase in Ac-H3-lys9 with maximal increase of ∼6-fold after 12 h exposure. Lung also showed ∼3-fold increase. In spleen, ethanol-induced Ac-H3-lys9 in all three ethanol-treated groups with similar increase (1.5- to 1.6-fold). Testes showed significant increase (3-fold increase) of Ac-H3-lys9 only at 1 h ethanol exposure. Ethanol had no affect on Ac-H3-lys9 in other tissues: kidney, brain, heart, stomach, colorectum, pancreas, and vessels. Ethanol had little effect on Me-H3-lys9 in all rat tissues examined. Conclusions: After in vivo administration of ethanol, analogous to binge drinking condition, the acetylations of H3-lys9 in rat tissues are not universal but tissue-specific events with different patterns of responses. Ac-H3-Lys9 in liver, lung, and spleen were significantly affected and it was demonstrated that ethanol causes this epigenetic alteration in rat tissues selectively.