Peroxynitrite (ONOO - /ONOOH) is a powerful and relatively long-lived oxidant that causes single-strand breaks in plasmid supercoiled DNA and induces mutations. Peroxynitrite can nitrate e.g. guanosine or tyrosine. The selenium-containing compound, ebselen, reacts with peroxynitrite. Here, we studied the effect of some selenium-containing compounds such as selenomethionine and selenocystine in comparison with their sulfur-containing analogs, methionine and cystine, on single-strand break formation of DNA, on Fe (III)/EDTA-catalyzed nitration of 4-hydroxyphenylacetic acid (4-HPA) and on the oxidation of dihydrorhodamine caused by peroxynitrite. Selenomethionine and selenocystine protected DNA from single-strand break formation, 4-HPA from nitration, and dihydrorhodamine from oxidation more effectively than their sulfur analogs. Sodium selenite exhibited no effect. Selenomethionine, selenocystine and ebselen showed similar protective activity on single-strand break formation in plasmid DNA and on the nitration of 4-HPA, while selenomethionine and ebselen inhibited the oxidation of dihydrorhodamine about 10 times more effectively than selenocystine. These observations may be a basis for a role of selenium-containing aminoacids in proteins in protecting against deleterious biological effects caused by peroxynitrite.