In our paper we present data on the induction of nitrosomethylurea focuses of aberrant crypts on experimentally altered thyroid status in mice and concomitant changes in the intestinal microbiota. Since the foci of aberrant crypts are an obvious prerequisite for long-range malignancy in colorectal cancer, the induction of colorectal cancer induced by nitrosomethylurea is the most appropriate model for investigating mechanisms of carcinogenesis. Male BALB / c male mice which were treated with nitrosomethylurea (NMU) for 24 weeks when also combined with L-thyroxin or propylthiouracil were used in the study. The results indicate that the incidence of aberrant crypt foci (FAC) was significantly higher for a group of animals which were treated with both NMU and L-thyroxin 38.9 ± 3.6%. At the same time the incidence of FAC with hyperthyroid status only without exposure to NMU was also high at 12.9 ± 4.2%. It was shown that the hypothyroid status had a significant protective effect on the intestinal epithelium when exposed to HMN – 16.1 ± 2.5%. A significant quantitative decrease in Lactobacillus spp. of microbiome was detected in groups of mice exposed not only to NMU, but also in animals with experimentally induced hyperthyroid status only. Mechanisms that contribute to the occurrence of an increased frequency of FAC in the context of hyper- and hypothyroid status are discussed. It was concluded that an increased incidence of foci of aberrant crypts and a decrease in the quantity of the normal microbiota are associated with hyperthyroid status which modulated upon administration of methylnitrosourea.