Many of the benefits of the antioxidant selenium can be attributed to its incorporation into selenoenzymes as the 21st amino acid, selenocysteine. Selenocysteine incorporation occurs cotranslationally at UGA codons in a subset of messages in prokaryotes, eukaryotes, and archaea. UGA codons are recoded to specify selenocysteine, rather than termination, by the presence of specialized cis- and trans-acting factors. Here we discuss the mechanism of selenocysteine insertion, the factors which affect efficiency of incorporation, and regulation of mRNA levels. Although much remains to be learned about the multiple factors affecting gene and tissue-specific regulation of the selenoenzymes, significant advances in this regard have been made in understanding the role of selenium status, the expression and selective modification of specific trans-acting factors, and the cis-acting sequences associated with each selenoenzyme message.