In photomedicine in some of cases radiation delivery to local zones through optical fibers can be changed for the direct placing of tiny optical sources like micro lasers or LED in required zones of ears, nostrils, larynx, nasopharynx cochlea or alimentary tract. Our study focuses on the creation of optoelectronic microdevices for local photo therapy. Now, they are taking pre-clinical trials in stomatology to treat inflammatory processes in the mouth cavity, in otolaryngology to treat otitis and for treatment of the gastro-intestinal tract. This paper is more emphasized on development optical microdevices for phototherapy of the gastro-intestinal tract. The influence of radiation from phototherapetic micromodules on composition of intestinal microflroa and the immunologic inspection of patients with dysbacteriosis of the intestine as a result of diseases of the gastrointestinal tract and after antibacterial therapy for other disturbances are studied. The obtained result are comparable with indices of the control group. At the same time, it should be noted that stimulation of growth of natural flora is recorded in the main group of patients which inhibits the activity of conditioned pathogenic microflora.