ABSTRACT— In primary teeth, root canal treatment is a time consuming and challenging procedure, particularly during the most important step in endodontic treatment which is the preparation of the canal. Pulpectomy is the treatment of choice in all the necrotic primary teeth. For better treatment protocol, advancing technology brought the rotary system to reduce the manual dexterity and improve the quality of treatment for pulpectomy. This study aimed to compare and assess the efficacy of cleaning and the time required for the instrumentation during the preparation of root canals of the primary molars using the rotary and the manual (conventional) systems. Thirty root canals of primary teeth were selected. These teeth submitted to access opening and then all the canals injected with Indian ink. Then, 48 hours later, the teeth were randomly classified into two groups: group A (n=fifteen tooth): where the manual preparation of the root canals was done by stainless steel K- files, while group B (n= fifteen tooth): consisted of the root canals that prepared with rotary two shape system. The total instrumentation time was measured using a digital stopwatch. After that, a disk bur was used to section the roots. Then, a digital camera was used to photograph the specimens to evaluate the root canal cleaning. The cleaning efficacy was compared at the coronal, middle and apical level. In the coronal third, rotary two shape system showed more removal to the ink than the K-file with statistical significant difference (p <0.05), however, for the middle third of the canal, no statistical difference was found between the two systems (p=0.05). While at the apical level, K-file showed more removal to the ink than the rotary two shape system and with statistical significant difference (p <0.05). Evaluation of the total samples revealed no statistical significant difference concerning the efficacy of cleaning between K-files and rotary two shape system files. The group that was rotary prepared took less time for the canal preparation as compared to the manual group (80.063 sec., 144.576 sec. respectively). No significant difference was found between the two systems concerning the cleaning efficacy. Instrumentation done by the rotary system took significantly less time than that of the manual. KEYWORDS: Cleaning efficacy, manual instrumentation, primary teeth, rotary instrumentation.