Relevance. The issue of quality endodontic treatment of teeth with complicated caries is still known as requiring thoughtful research. A significant percentage of periodontitis occurs in the area of furcations of multi-rooted teeth, sometimes alone, but more often as combined with apical periodontitis. Among the number of unsolved tasks, there is question about furcation areas and in particularly their antiseptic treatment and obturation in the complex treatment of chronic apical periodontitis of multi-rooted teeth. Aim: to investigate the histo-morphological features of the furcation area of the first, second molars of the upper and lower jaws and, according to the results of the experimental study, to develop a scheme of complex treatment of chronic apical periodontitis of multi-rooted teeth. Materials and methods. Ten first and second molars of both jaws not affected by fluorosis and removed according to orthodontic or surgical indications in patients aged from 25 to 50 years, were used for this study. In the first stage, transverse and longitudinal sections of the molars were made using diamond-coated separation disks. Using an orthopaedic tip, the first half of the molars were cut longitudinally in the mesio-distal direction with separation disks, under water cooling. The other half of the molars were cut transversely along the neck of the tooth and histochemically stained. In the second stage of the study, we used the experimental application of photodynamic therapy for antiseptic treatment of furcation channels and sealing them with citrate buffer. For this purpose, the next two first and two second mandibular molars were selected, respectively dissected in two planes. Samples were fixed in a vertical position; cotton rolls soaked with 2% methylene blue were placed onto the bottom of each half for 30 s., 1 min., 5 min., and 24 h. In this study we used light binocular stereoscopic microscope MBS-9; histochemical dyes: CHIC-thionine, ammonia silver solution "Argentat", reducing agent (hydroquinone), methylene blue, device "UFL - 122" company "Lux Dent", citrate buffer solution and white clay. The results were recorded with a digital camera mounted on a microscope tube. Results and discussion. The results of histochemical examination of ten molars showed the presence of furcation channels in four teeth. Two samples were stained with CHIC-thionine, the others were stained with two-component "Argenate". The selected samples were dissected in the sagittal plane through the area of localization of the furcation channels and studied under the microscope (magnification: 8x32). In teeth dissected in the transverse plane, the crown and mouth pulp were instrumentally removed without dilation of the root canals and stained accordingly. Thus, when modelling the stage of photodynamic treatment using a 2% solution of methylene blue, there is a significant filling of furcation channels and root canals along their entire length. The photosensitizer 2% methylene blue at the exposure of 30s demonstrates the highest efficiency at the minimum staining of surrounding fabrics. The microscopy was performed to confirm the ability of the photosensitizer to penetrate into the furcation channels at х8 – х32 magnification. After the experimental filling of furcation channels and root canals, we can see clear white stripes along their entire length on the dentin surface of the longitudinal section of the root; these stripes are obliquely directed towards the canal surface and consist of numerous dentinal tubules impregnated with citrate buffer. Numerous thin white lines are clearly visible on the surface of the section that run in parallel, tangentially through almost the entire thickness of the root wall and end up their course in the area around the peripulpal dentin. This indicates the formation of calcium citrate in the root canal that tightly covers its entire surface impregnating the dentinal tubules and completely fills them along their entire length. Therefore, the experimental model of using 2% methylene blue photosensitizer at a 30 s. exposure for photodynamic therapy and citrate buffer for obturating furcation and root canals can be applied in the treatment of patients with chronic apical periodontitis and lesions of the furcation area. Conclusions. Thus, morphological studies of the first and second molars of both jaws have shown the presence of furcation channels, which anatomical structure is quite complex and demanding in terms of their antiseptic treatment and filling. Therefore, we developed new effective for disinfection and obturation techniques including applying photodynamic therapy for disinfection of furcation channels and citrate buffer for their obturation.