The colon microflora was investigated by PCR method in real time before and after planned operation in 38 patients with colon cancer. A multifactor analysis showed absence of statistically significant dependence of revealed changes in microflora from sex, age of patients, volume and method of surgery, presence of tumor stenosis and infiltrate. An anaerobic imbalance was often registrated in postoperative period, especially after antibiotic prophylaxis and therapy. Clostridium difficile and Clostridium perfringens were often detected in patients with tumor of the right part of colon (p<0,05). The irritable colon syndrome was noted in 34% (n=13) patients after one month. Сlostridial infection was revealed in majority of these cases. The authors recommend to perform the microbiota analysis before and after surgery.