A common feature of the photosensitizers in current or proposed use for photodynamic therapy (PDT) is their lipophilicity which promotes their accumulation in cellular membranes. In spite of the absence of observable photosensitizers in the nucleus, photodynamic activation of photosensitizer-loaded cells produces substantial amounts of DNA damage. With either porphyrins or phthalocyanines as photosensitizers, the yield of DNA single-strand breaks plus alkali-labile sites (SSB) is less than that resulting from an equitoxic dose of ionizing radiation; however, these same photodynamic treatments produce high yields of DNA-protein crosslinks (DPC), which are not repaired during post-treatment incubation of the cells, in contrast to the DPC produced by ionizing radiation. Initial yields of DPC after photodynamic treatment of murine lymphoma L5178Y cells sensitized by chloroaluminum phthalocyanine (AlPcCl) are greater in the relatively PDT-sensitive strain LY-R as compared to the relatively PDT-resistant strain LY-S. Photodynamic treatment sensitized either by AlPcCl or by Photofrin II is mutagenic at the thymidine kinase (tk) locus in one or more sub-strains of LY-R and LY-S. With Photofrin II, the induction of mutations has been observed in the tk+/- heterozygous strains LY-R16 and LY-S1, but not in the hemizygous tk+/0 strain LY-R83. This pattern of strain-specific mutagenesis is found for other agents, such a ionizing radiation, which produce a high proportion of multi-locus lesions. With AlPcCl, mutation induction is found in strains LY-S1 and LY-SR1, but not in either of the sub-strains of LY-R. Treatment of strains LY-R and LY-S with identical doses of AlPcCl and red light results in degradation of the DNA, which occurs earlier and to a greater extent in the more PDT-sensitive strain. Examination of the size of the DNA during the period of degradation revealed a series of fragments with sizes which were multiples of approximately 190 bp. This suggests that PDT treatment of L5178Y cells induces the process known as apoptosis, or programmed cell death, in which endonucleolytic scission of the DNA occurs in the internucleosomal linker region. DNA degradation is also stimulated by treatment of murine L929 fibroblasts with phthalocyanine and light but not by gamma- irradiation alone. Combined treatment with a minimally lethal dose of PDT and a dose of gamma-radiation producing 90% cell death results in the induction of a PDT-type cell death in a substantial portion of the cells. When the level of programmed cell death is very high, the recovery of mutants may be compromised. Thus, PDT appears to produce extensive DNA damage, but events at other cellular locations may alter the expression of that damage.