Considerable progress has been made in expanding the number and nature of genetically encoded amino acids in Escherichia coli, yeast and mammalian cells in the past four years. To date, over 30 unnatural amino acids have been cotranslationally incorporated into proteins with high fidelity and efficiency by means of a unique codon and corresponding orthogonal tRNA-aminoacyl-tRNA synthetase pair. The incorporated amino acids contain spectroscopic probes, post-translational modifications, metal chelators, photoaffinity labels and unique functional groups. The ability to genetically encode additional amino acids, beyond the common 20, provides a powerful approach for probing protein structure and function both in vitro and in vivo, as well as generating proteins with new or enhanced properties.