Objective: To compare via a split-mouth randomized clinical trial the efficacy of 1% chlorhexidine gel, calcium hydroxide/camphorated paramonochlorophenol (Callen PMCC), and a one-visit endodontic treatment against mutans streptococci and anaerobic bacteria found in primary molars with necrotic pulps and to assess clinical success rates after 12 months. Method and Materials: Pre- and posttreatment intracanal samples were collected from 37 teeth (from 21 children) for analysis of the number of mutans streptococci and anaerobic bacteria. Clinical and radiographic criteria were analyzed to determine treatment outcome. Results: Chlorhexidine gel significantly reduced mutans streptococci levels (P = .010), whereas Callen PMCC significantly reduced the levels of anaerobic bacteria (P = .002). No differences in the reduction of mutans streptococci (P = .187) and anaerobes (P = .564) were observed between groups. The clinical success rates were 85.71% (Callen PMCC), 78.57% (chlorexidine gel), and 77.77% (one-visit treatment). Conclusion: Teeth treated with Callen PMCC presented the highest clinical success rate. The 1% chlorhexidine gel, as well as calcium hydroxide/camphorated paramonochlorophenol, presented limited efficacy in reducing bacteria from necrotic primary root canals. Keywords: calcium hydroxide, camphorated paramonochlorophenol, chlorhexidine, primary molars, pulp necrosis