Aim. To identify micronutrient deficiencies in patients with functional bowel diseases (FBD) and to reveal their correction with functional foods and probiotics. Subjects and methods. The health status was evaluated in 90 patients aged 18 to 67 years with FBD. All the patients were randomized into 3 groups according to the treatment regimen. Group 1 took Amaltea goat's milk 200 ml/day during basic therapy; Group 2 received multispecies and multistrain RioFlora Balance probiotics in addition to the above components; Group 3 (a control group) had traditional basic dietary therapy. All the groups continued their treatment for 14 days. Results. The performed examinations have demonstrated that diet-based treatment fortified with goat's milk and multispecies probiotics makes it possible to more promptly achieve remission and to level off clinical manifestations than in the control group. The patients using multispecies probiotics versus the control group showed a reduction in fat-soluble vitamin deficiencies and a considerable improvement in quality of life. Conclusion. FBD lacks a specific clinical picture and may be masked as lactase deficiency, which commonly leads to noticeable limitations in patients' diet and favors the development of vitamin deficiency. Of particular concern is the development of vitamin D deficiency in young patients, which may result in the early development of osteoporosis in the future. To specify the composition of enzymes in the patients gives grounds to refuse restricted diets, and the dietary addition of functional foods (goat's milk fortified with vitamins and minerals), particularly in combination with multistrain probiotics, produces a pronounced clinical effect and eliminates fat-soluble vitamin deficiencies.