Human metaphase chromosomes, substituted with 5'-bromodeoxyuridine (BrdUrd) for one, two or three rounds of replication, were briefly pretreated with ultraviolet light (UV), in the presence of 33258 Hoechst, and subsequently digested with either exonuclease III or S1 nuclease. Pretreatment alone was not sufficient to induce sister chromatid differential staining (SCD), but allowed subsequent digestion with exonuclease III or S1. Such enzymes were found to induce SCD with ethidium bromide, as unifilarly BrdUrd-substituted chromatids (TB) were more resistant than bifilarly substituted chromatids (BB). Other experiments with DNase I or the AluI and HaeIII restriction endonucleases showed that only HaeIII was capable of inducing SCD by attacking BB more than TB chromatids preincubated with UV in the presence of Hoechst. SCD with exonuclease III/S1 nuclease seems to be due to (1) UV-induced DNA debromination occurring twice in BB as opposed to TB chromatids, and (2) alteration of chromatin protein structure occurring to a different extent in differently BrdUrd-substituted chromatids. Our findings with endonucleases, on the contrary, may depend on the capacity of enzymatic cleavage to cancel the different protein alterations induced differentially by UV in TB as opposed to BB chromatids.