Background: The present study was conducted to compare Kedo- S rotary file system, universal protaper and manual instrumentation in pediatric patients. Materials & Methods: The present study was conducted on 60 children age ranged 4- 8 years of both gender. Patients were divided into 3 groups. Group I (N = 20): The root canals were instrumented with Kedo-S paediatric rotary files as per manufacturer’s recommendation. Group II (N = 20): the root canals were instrumented with Protaper and group III root canals were manual hand files. Obturation was done as per standardized criteria. Results: The quality of obturation was under fill in 12% in group I, 13% in group II and 6% in group III, optimal 68% in group I, 60% in group II and 54% in group III, over fill 20% in group I, 27% in group II and 40% in group III. The difference was significant (P< 0.05). The mean instrumentation time in group I was 45.8 seconds, in group II was 56.4 seconds and in group III was 65.2 seconds. The difference was significant (P< 0.05). Conclusion: Kedo- S files were better in terms of instrumentation time and obturation as compared to protaper and manual files in children. Key words: Kedo- S files, Protaper, Manual files