Since viable bacteria can persist in tooth cavities regardless of the technique used for caries removal, the objective of the present randomized clinical trial was to examine the microflora of primary teeth treated by complete or partial removal of carious dentin. Deciduous molars with acute carious lesions in the inner half of dentin and vital pulp were randomly divided into two groups of 16: complete removal, in which the carious dentin was completely removed with the help of a caries detector dye, and partial removal, in which the carious dentin was completely removed from the dentinoenamel junction and lateral walls, while the necrotic carious dentin from the cavity floor was only removed superficially. Dentin samples were obtained with a sterile No. 3 bur after caries removal and 3–6 months after protection with calcium hydroxide cement and restoration of the cavities with resin composite. The samples were stored in thioglycolate. Decimal dilutions were then prepared and seeded for the enumeration of Streptococcus spp., mutans streptococci, Lactobacillus spp. and total microorganisms. Before sealing, a larger number of microorganisms was detected in teeth submitted to partial caries removal compared to the complete removal group. However, after sealing the level of colonization was similar in the two groups for all microorganisms studied. The results suggest that persistence of bacteria does not seem to be a reason for reopening of cavities in deciduous teeth after partial caries removal.