Aim: To evaluate and compare the antimicrobial efficacy of commonly used endodontic irrigation solutions against bacterial and fungal isolates recovered from infected root canals in patients with apical periodontitis, in order to determine their relative effectiveness against clinically relevant endodontic microorganisms. Materials and Methods: The strains of opportunistic microorganisms representing the optionally anaerobic transient microflora of the oral cavity were used in the study. 11 chemical solutions used to eliminate microorganisms in the root canal, were applied in the microbiological study. Microbial cultures were isolated from the infected root canal and identified on the basis of morphological, cultural properties and such biochemical microtests as “STAPHYtest 16”, “STREPTOtest 16” (Lachema, Czech Republic) and test systems VITEK 2 GP and VITEK 2 YST (biomerieux, France) using VITEK 2 Compact analyzer. Results: Comparing the effect of irrigation solutions on S.aureus MSSA bacteria, such irrigant as Chlorhexedin 2% (Endohex) provided the most positive result Hypochlorite 5.25% (Cerkamed) provided a positive effect on C.ablicans as well constituting 88.82±1.65 in comparison with Chlorhexedine 2% (29.22±0). Citric acid 40% (Cerkamed) was the best to eliminated S.gordonii (27.28±0.35). However, Maleic acid 6% showed the least effect on it (6.55±0.45). Hypochlorite 5.25% (Cerkamed), Hypochlorite 6% Chloran showed the best influence on the Candida group, while Citric acid 40% showed the lowest influence. Conclusions: The conducted microbiological studies showed a diverse effect of irrigation solutions on groups of different microorganisms causing periodontitis. The obtained results provide an opportunity to select differentially irrigation solutions for the elimination of microorganisms detected in the root canals. A positive result of the elimination of irrigation solutions on microorganisms causing periodontitis is observed.