The antimicrobial activity of 0.4% papaine gel (FCF-USP), an antibacterial product derived from 3.3% castor oil (IQSC-USP), and 0.5% sodium hypochlorite (FORP-USP) was evaluated in teeth with radiographically visible pulpal necrosis and periapical lesion in vivo. After cavity access, under aseptic conditions, a first harvesting was performed. The 3 irrigating solutions were used for biomechanical preparation. After 72 hours, a second harvesting was performed, also under aseptic conditions. The number of colony forming units (cfu) was counted with a stereomicroscope under reflected light. Castor oil and 0.5% sodium hypochlorite presented similar antimicrobial activities for the reduction of the anaerobe number, S. mutans and streptococci; however, the papaine gel showed lower activity. We conclude that both castor oil and sodium hypochlorite are effective as antimicrobial agents and can be used in the treatment of root canals with pulpal necrosis.