Vaginal disorders associated with systemic chemotherapy arise by direct inhibition of the resident microbiota (dominated by lactobacilli) or, possibly, by induction of prophages harbored in their genomes, leading to cell lysis. In the present study, proficient Lactobacillus phages could not be isolated from vaginal exudates. However, lysogeny appeared to be widespread, although about half of the strains harbored prophage sequences that were not responsive to SOS activation. In other cases, prophage induction was achieved, but viable phages were not generated, despite the fact that the induced supernatants of some strains were bactericidal. In one case, this activity was accompanied by the production of a bacteriophage subsequently identified as a member of the family Siphoviridae (isometric capsid and long non-contractile tail). Most of the lactobacilli tested generated hydrogen peroxide, which acted as an inducer of the SOS response, suggesting that H2O2 selects for strains that harbor SOS-insensitive, defective prophages, which are thus unable to promote vaginal lactobacilli phage-induced lysis.