Aim. The research was carried out to create and evaluate the effectiveness of the rehabilitation algorithm of children who underwent a surgery on the colon and anorectal area.Materials and methods. We have experience in rehabilitation of 245 patients aged from 8 months to 15 years with anorectal agenesis and Hirschsprung's disease. To assess the effectiveness of the proposed algorithm of rehabilitation measures we formed 2 identical groups according to age, sex and nosology indicators. The main group consisted of 136 children with abovementioned pathology. Rehabilitation measures were carried out according to the developed algorithm. It included early bougienage, general and local physiotherapy, correction of intestinal dysbiosis by selective decontamination, relief of water-electrolyte and metabolic disorders. The control group consisted of 109 patients. Rehabilitation was carried out according to the traditional methods. Results. When comparing the results of rehabilitation, the following data were obtained: therapeutic and preventive bougienage was carried out for 18.34±1.29 months in patients of the control group and for 9.56±0.94 months in children of the main group. The duration of anal sphincter insufficiency treatment in the control group was 23.48±1.95 months and only 11.29±1.07 months in the main group. The timing of the correction of dysbiosis in patients of the control group was 36.25±2.17 months and 14.36±1.14 months in children of the main group. The duration of electrolyte disorders and metabolic disorders correction in the control group was 14.16±0.57 months and 6.34±0.28 months in the main group.Conclusion. The application of the developed algorithm of rehabilitation measures made it possible to reduce their duration by more than 2 times according to all the studied criteria. It allows us to recommend the created rehabilitation algorithm for wide clinical application.