Background: Colorectal cancer (CRC) is one of the leading causes of death in both men and women worldwide. According to different studies, infectious agents or microbiota dysbiosis can play a role in CRC progression. Objective: This study aimed to evaluate the prevalence of Enterococcus faecalis, Lactobacillus acidophilus, and Lactobacillus plantarum in people with polyps or CRC compared to healthy individuals. Methods: In this study, 60 biopsy samples were collected from three groups, including patients with CRC, polyps, and healthy people. The genomic DNA was extracted from the collected samples and amplified by polymerase chain reaction (PCR) to detect E. faecalis, L. acidophilus, and L. plantarum. In the next step, quantitative Real-Time PCR was used to evaluate the copy number of the bacteria in the studied groups. Results: There was no statistically significant difference between the studied groups regarding age and gender (P > 0.05). The mean number of E. faecalis was higher in patients with CRC than in patients with polyps and healthy individuals (P < 0.05). Also, the mean numbers of L. acidophilus and L. plantarum were higher in healthy individuals than in patients with polyps and CRC (P < 0.05). Conclusions: Our findings indicate that L. acidophilus and L. plantarum in people with a family history of CRC and patients with polyps may effectively prevent or reduce CRC progression.