Aim: Root canal treatment is often carried out in deciduous teeth to relieve pain and make the tooth functional.The main goal of instrumentation in a root canal treatment is to facilitate effective irrigation, disinfection, and filling. Sodium hypochlorite is a widely used irrigant and has been demonstrated to be an effective agent against broad spectrum of bacteria. However its toxic effects on vital tissues can result in haemolysis, skin ulceration and necrosis. The use of diode laser for endodontic applications has been investigated and proven for its efficacy in root canal sterilization. Therefore, this clinical study was conducted to evaluate and compare the efficacies of 5.25% sodium hypochlorite (NaOCl) and 810nm diode laser as disinfectants in root canals of primary teeth. This study evaluated the microbial count and the clinical success of the treatment. Materials and Methods: In 40 subjects selected based on the inclusion and exclusion criteria, Pulp tissue was extirpated from the canals and samples collected using sterile absorbent paper points . Then they were randomly divided into two groups. In Group 1, canals were prepared and irrigated with 5.25% of sodium hypochlorite, and in group 2 canals were prepared and disinfected with 810nm of diode laser. The contents of canals were collected again with a sterile paper point .Samples taken before and after procedures were cultured, and the colony-forming units (CFUs) were counted. The data was evaluated using independent sample test and paired sample test. Patients were recalled for clinical and radiographic evaluation after 3 and 6 months. Results: There was a significant difference between the mean CFU of laser and sodium Hypochlorite ( p<.001). Clinical evaluation after 3 and 6 months showed no pain, swelling, sinus tract or mobility .Radiographically too there was absence of premature exfoliation, periodontal widening, internal/external resorption and periapical or furcal radiolucency. Conclusion: Both 810nm diode laser and 5.25% sodium hypochlorite were effective in reducing bacterial count in root canals of primary teeth. However 810nm diode laser reduced microbial count of root canals more as compared to 5.25% NaOCl.