Background: The successful treatment of root canal is contingent upon the complete eradication of the bacterial infection. This study aims to assess the antimicrobial efficacy of a rotary and manual filing system in primary molar teeth when NaOCl 1%, NLE 100% and saline were employed.

Martials and methods: This randomized controlled clinical trial included 60 primary molars indicated for pulpectomy from 30 children aged between 4-7 years old, with two contralateral primary molars indicated for pulpectomy, who were randomly selected from the clinic of Pediatric Dentistry, Mansoura University. The selected children were divided into two main groups randomly, based on filing system group I for manual and group II for rotary. Then 3 equal subgroup according to irrigant; subgroup I A and II A , subgroup I B and II B and subgroup I C and II C. normal saline ,100%NLE, 1%NaOCl respectively .

Results: The mean pre- and post-preparation (CFU/ML) in various subgroups exhibited a highly statistically significant difference. The NaCl group exhibited the greatest percentage change, followed by the Neem group, and the Saline group exhibited the least change. Neem and NaOCl are significantly different from saline but do not significantly differ from each other. Across both methods (manual and rotary), NaOCl consistently shows the highest effect, while saline shows the lowest effect and neem in between.

Conclusions: The root canal flora was significantly decreased by both rotary and manual files. AF baby rotary files demonstrated a more effective reduction of microbes in root canals than manual instrumentation.