Several recent studies have suggested that epigenetic changes induced by the environment can be inherited through the germline from the parent to the progeny. For example, a high fat paternal diet in rodents changes the insulin and glucose levels in serum of the offspring and induces an abnormal response after glucose or insulin injections. Though phenotypic changes have been found in the offspring, the mechanisms remain largely unclear. We hypothesized that the fat content of a diet may have an impact on chromatin composition during gamete development and this may have the potential to influence the reprogramming process that takes place during the transition from spermatogonia to spermatids. Using an obesity mouse model, we examined treatment of high versus low fat diet in C57BL/6J male mice and its effect on H3 retention in spermatozoa and examined mRNA expression of several fat synthesis related genes in the liver of offspring. In order to address molecular mechanisms of how diet induced effects may possibly be transferred to the next generation, we examined the chromatin of diet treated fathers. We first addressed the question of whether CG methylation is altered in spermatozoa at differentially methylated regions (DMR) of genomic imprinted genes. Using bisulfite sequencing we examined CG methylation at seven known ICRs (Imprinting Control Region) which show complete CG methylation in sperm or are excluded from CG methylation in sperm. The patterns did not reveal significant methylation differences comparing genomic DNA derived from HFD to LFD fathers. Although most of the histone proteins are replaced by protamines during spermatogenesis, about 1-5% of histones are retained in sperm and can shuttle to the progeny. To address the effect of diet on histone content in sperm, we performed chromatin immunoprecipitation (ChIP) of sperm using specific antibodies against histone H3 followed by high-throughput sequencing. We observed greater H3 enrichment in sperm of high fat diet parents compared to low fat diet parents, indicating enhanced H3 retention during sperm generation after high fat diet treatment. The genes with the highest H3 enrichment at their promoter region are involved in the regulation of embryogenesis. Furthermore, we performed ChIP-Seq for the H3K4me1 modification in sperm and found specific retention of H3K4me1in high fat samples at a discrete subset of genes that encode for embryonic transcriptional regulators. Finally, we examined mRNA of 20 selected genes that play a role in fatty acid metabolism and the oxidative stress response in the liver of offspring. We found seven (out of 20) genes were differentially expressed in high fat diet progeny compared to low fat diet progeny including MT1, MT2, Fasn, Por and Acaca. Obesity is associated with a number of human diseases including diabetes, cardiovascular diseases, cancer and arthritis. Obesity is in part induced by dietary choices. Our study suggests that high fat dietary exposure in an animal model can modulate histone composition at regulatory genes implicated in developmental processes. Furthermore, high fat dietary exposure of the parent can modulate the gene expression profile in the progeny.