Extracted human teeth provide the closest approximation to teeth in situ and play important roles in dental education and materials research. Since extracted teeth are potentially infectious, the Centers for Disease Control recommend their sterilization by autoclaving or disinfection by formalin immersion to ensure safe handling. However, autoclaving is not recommended for teeth with amalgam fillings and formalin is hazardous. The goal of the present study was to investigate the potential of peracetic acid (PA) as an alternative method to achieve reliable disinfection of freshly extracted teeth. A total of 80 extracted teeth were collected for this study. Whole teeth were incubated in one of four solutions for defined periods of time: sterile water (2 weeks), formalin (2 weeks), PA 1000 ppm (2 weeks), and PA 2000 ppm (1 week). After sectioning, the crown and root fragments were transferred into separate tubes containing brain–heart infusion broth and incubated at 37 °C under anaerobic conditions for 72 h. Absence of broth turbidity was used to assess effectiveness of disinfection. No turbidity was observed in any of the formalin-treated or peracetic acid-treated samples, signifying complete disinfection. Our results indicate that PA can effectively disinfect extracted human teeth, providing a reliable alternative to formalin and autoclaving.