Infectious agents have varying susceptibilities to thermal inactivation and/or mechanical removal from cages by the use of heated, pressurized water. In this study, we tested whether 5 specific infectious organisms (Candidatus savagella [segmented filamentous bacterium (SFB)], Helicobacter sp., mouse norovirus (MNV), Tritrichomonas sp., and Entamoeba muris) could survive the cage wash process and still infect naïve mice. These 5 organisms were chosen due to their prevalence in rodent colonies, environmental stability, and/or potential to influence experimental outcomes. Cages that had housed mice shedding all 5 organisms were assigned to 1 of 3 treatment groups: 1) sanitization in a tunnel washer followed by autoclaving (121 °C [250 °F] for 20 min; n = 40 cages); 2) sanitization in a tunnel washer (82 °C [180 °F] for an average of 30 s; n = 40 cages); or 3) control (bedding change only; n = 40 cages). The presence of these agents in the cage was assessed by performing PCR on swabs of the empty soiled cage interior before and after the treatment. In addition, to determine if any residual nucleic acid was infectious, 2 Swiss outbred (J:ARC(S)) female mice were housed for 7 d in cages from each treatment group. The above procedures were then repeated so that every week each pair of J:ARC(S) mice (n = 10 pairs of mice/treatment group) were housed in another cage that underwent the same treatment; this was done for a total of 4 consecutive, 1-wk-long periods. Swabs collected from soiled cages were PCR-positive for SFB, Helicobacter, MNV, Tritrichomonas, and Entamoeba in 99%, 97%, 39%, 63%, and 73% of the cages tested, respectively. Cages in the tunnel wash group that were PCR-positive for SFB, Helicobacter, Tritrichomonas, and Entamoeba before treatment remained PCR-positive in 8%, 15%, 43%, and 10% of positive cages, respectively. None of the cages from the autoclave group were PCR-positive for any of the agents after treatment. None of the mice housed in cages in either the autoclave or tunnel wash groups became infected with any of the agents. However, 80%, 60%, and 100% of the pairs of mice housed in untreated cages were PCR-positive for SFB, MNV, and Entamoeba, respectively. None of the mice housed in untreated cages were positive for Helicobacter or Tritrichomonas. Our results suggest that nucleic acids from these bacterial and protozoal organisms may remain in cages after mechanical cage washing, but these nucleic acids are not infectious, and autoclaving is not necessary to prevent transmission.