A set of DNA probes has been developed to study the genes for Shiga-like toxins (SLT) and the bacteriophage from which these toxin genes were isolated. Under stringent conditions of hybridization (80 to 90% homology), these probes detect strains containing (i) SLT I-related genes, (ii) SLT II-related genes, (iii) phage sequences from the SLT I-converting phage H19A/933J, and (iv) phage sequences from the SLT II-converting phage 933W. Strain characterization by hybridization with the toxin gene probes was as accurate as methods that used toxin-specific antibody to determine toxin synthesis. Screening of different gram-negative bacteria with the toxin probes revealed that only two species carry sequences related to the SLT genes, Escherichia coli and Shigella dysenteriae 1. These results indicated that the lower levels of toxin activity observed in shigellae other than S. dysenteriae 1 are due to a gene(s) that is genetically distinct from that which encodes Shiga toxin. Analysis of enterotoxigenic, enteroinvasive, enteropathogenic, and enterohemorrhagic E. coli indicated that SLT genes are found primarily in the enterohemorrhagic E. coli strain group. Use of both the toxin and the phage probes has identified a variety of genotypic combinations of phage and toxin sequences which differ from those observed for the original toxin-converting phage isolates, for E. coli O157:H7 strain 933, and for E. coli O26:H11 strain H19.