Ethyl methanesulfonate (EMS) killed wild-type Bacillus subtilis spores as rapidly as spores lacking small, acid-soluble proteins (SASP) of the a/b type (ab spores), and 20% of the survivors had obvious mutations. A recA mutation increased the EMS sensitivity of wild-type and ab spores similarly but reduced their mutagenesis; EMS treatment of dormant spores also resulted in the induction of RecA synthesis during spore germination. EMS generated similar levels of alkylated bases in wild-type and ab spore DNAs, in purified DNA, or in DNA saturated with a/b-type SASP. Ethylene oxide (EtO) also generated similar levels of base alkylation in wild-type and ab spore DNAs. These data indicate that EMS and EtO kill spores at least in part by DNA damage but that a/b-type SASP, which protect DNA against many types of damage, do not protect spore DNA from base alkylation.