Background The aim of this study was to investigate the efficacy and safety of the novel complex drug, consisting of released-active form of antibodies to S-100 protein, tumor necrosis factor-α and histamine, (Kolofort) under outpatient conditions in patients with functional dyspepsia (FD), irritable bowel syndrome (IBS), and their combination. Methods The subject of the observational noninterventional retrospective program was the data of 14,362 outpatient records of patients with diagnosed FD, IBS, and/or their combination who received the drug Kolofort in monotherapy for 12 weeks, 2 tablets twice a day. To assess the presence and severity of symptoms of functional disorders of the gastrointestinal tract (FD GIT), a questionnaire “7*7” developed by a working group from the Russian Gastroenterological Association was used. The evaluated parameters included the proportion of patients: who had a reduction in the number of points by 50% or more; who have decreased the severity category of the condition; who have switched to the “healthy” and “borderline ill” severity categories;and the change in the number of points in domains 1–7. Results The final efficacy analysis included data from 9,254 patients. A decrease in the number of points by 50% or more was observed in 80.45% of patients with FD, 79.02% of patients with IBS, and in 83% of patients with both IBS and FD. A decrease in the severity category of the condition at the end of therapy was noted in 93.35% of patients with FD, in 93.80% of cases in patients with IBS, and in 96.17% of cases in patients with a combination of IBS and FD.A total of 94 adverse events (AEs) were reported in 80 patients (0.65%). Conclusion The COMFORT program has demonstrated the positive effect of treatment in the majority of patients with IBS and FD and their combination in real clinical practice.