ABSTRACT Nowadays there is evidence that animals are exposed to microplastics (MPs) via food, however there is not much known about their effect on tissue of gastrointestinal tract and on gut microbiome. In this study, adult male rats were fed with polyethylene MPs, mixed with standard pellet food for 24 days at different concentrations ranging from 0 to 1000 μg/day. At the end of experiment, rats were euthanized and histopathological investigation using light and electron microscopy and the gut microbiome was analyzed using MiSeq 16S rRNA amplicon sequencing. Microscopic analysis revealed significant impact of MPs on the intestine, including visible changes to the crypt area as well as reduction in mucus secretion. Autophagic vacuoles were observed in the livers of the rats fed with MPs at 100 µg/day. Oxidative stress was evident in rats fed with 1000 µg/day of MPs, as indicated by the presence of myeloid bodies in both intestinal and hepatic cells. The gut microbiome was also affected by MPs. Although, no distinct clusters were formed when the bacterial communities in the different treatments were ordinated by multidimensional scaling (NMDS), the diversity indices including operational taxonomic unit (OTU) richness and Chao1 exhibited an increasing trend with increasing MPs concentration. Pearson correlations revealed a linear increase in the relative sequence abundance of Clostridia (R=0.036, P=0.003) with increasing MPs concentration, but not in the case of other bacterial groups,. Lactobacillus faecis was the most abundant OTU in the entire dataset, and its relative abundance decreased significantly with increasing MPs concentration. We conclude that exposure to MPs can disrupt cellular function and disturb microbiome balance, and in the event of prolonged exposure, organisms might experience unpredictable effects.