Objectives: To evaluate the disinfecting effect of sodium hypochlorite during partial caries excavation of deciduous teeth in vitro. Counts of microorganisms in dentin samples served as primary endpoint. Methods: 12 freshly extracted primary teeth from children with early childhood caries were sectioned in three parts and one of each part was treated as follows within two hours after extraction: 1. partial caries excavation (PE), 2. partial caries excavation with 1% NaOCl (PEC) and 3. complete caries excavation (CE) as a positive control. A round bur in a torque controlled handpiece was used for the excavation procedures under simulated clinical conditions at a room temperature of 37°C. Prior to collecting the dentinal debris, samples were rinsed with 65 ml ringer lactate. Vortexed dentin samples were anaerobically grown on blood agar for total viable counts and MSB and Rogosa agar for mutans streptococci and lactobacilli species respectively. Results: Compared to the CE group total viable counts were significantly higher in the PE and lower in the PEC group (p0.05). In the PEC group three samples showed no bacterial growth, lactobacilli were not identified in 11 samples and mutans streptococci were not found at all. In the CE group a relevant amount of cfu was detected on every culture media. Conclusions: Application of sodium hypochlorite during partial caries excavation will disinfect the remaining dentine more effectively than complete caries excavation and should be considered as a clinical standard like it is for root canal treatment. Keywords: excavation, Carious dentin, disinfection, Oral Pathogenic Bacteria, sodium hypochlorite