The endodontic triad comprises of cleaning and shaping, disinfection and obturation. Success of root canal therapy is majorly achieved by proper cleaning and shaping. However, elimination of bacterial contaminants as well as necrotic debris of the canals requires the adjunctive use of irrigants. To achieve a satisfactory biological and mechanical preparation proper selection of endodontic instruments and irrigants is necessary. In this study we are comparing and evaluating cleaning efficacy of endofiles (K-files and handprotapers) and root canal irrigants (sodium hypochlorite and chlorhexidine) by microbial quantification. Root canal samples were collected in autoclavable bottles containing transport media (nutrient broth) and samples were cultured in tryptose soya agar at incubation temperature of 37°C for 24-48 hours and colonies were counted with digital colony counter. The significance of this study is to help the clinician select proper instrument and irrigant which minimize the failure rate of root canal treatment for the benefit of patients.