Statement of problem: New Ni-Ti rotary instrument systems have been designed for ease of canal preparation in permanent teeth. Evaluation of the ability and effectiveness of such newely introduced devices in pulp treatment of deciduous teeth seems to be logic and necessary approach as well.Purpose: The purpose of this study was to compare the manual (K-file) and rotary (protaper) techniques on cleaning ability and instrumentation time in deciduous molar teeth.Materials and method: After injection of Indian ink into root canals of 49 teeth of 56 selected deciduous molars, the teeth were randomly devided into three experimental groups (14 teeth and 42 canals in each), and two control groups (each of 7 teeth and 21 canals). Canal preparations were done manually (K-files) in group I, and by protaper rotary files in group II. In group III canals were only irrigated with normal saline, but no cleaning or irrigation of the canals were done in groups IV and V (control groups). Instrumentation time was recorded for groups I and II. After clearing procedure, canals contents were observed with a stereomicroscope at X10 magnification, and results were analyzed using T-test, ANOVA and Tukey HSD test.Results: Mean cleaning amount of apical, midle and coronal thirds of the canals for protaper rotary files group (II) was more than that of manual K-files group (I) and normal saline group (III). The differences between groups I and II and groups II and III were statistically significant (P<0.001). Mean cleaning amount of all parts of canals for K-file manual instrumentation group (I) was more than that of normal saline group (III). Statistical difference between groups I and III was also significant (p<0.001). mean recorded instrumentation time in group II (rotary protaper group) was 70 seconds, while it was 130 seconds for manual K-file instrumentation group (p<0.001).Conclusion: results suggest that rotary protaper can efficiently be used for endodontic treatment of deciduous teeth.Key words: Manual K-files, Rotary protaper files, Cleaning ability, Instrumentation time, Deciduous Molars