tRNAs are remarkable among the natural nucleic acids in the cell in that they contain a large percentage of modified nucleosides. tRNAs are further distinguished in that there is an abundance of chemical diversity with over 100 different nucleoside modifications characterized. These modifications vary from the common base and sugar methylated nucleosides to hypermodified nucleosides containing, for example, sulfur, isoprene groups, and amino acid modifications. Modifications in the tRNA anticodon region are particularly prevalent and directly affect tRNA function by modulating the codon-anticodon interaction. In addition to the normal role of tRNA for protein synthesis, tRNAs have an interesting function as the obligate primers of retroviral reverse transcription. In HIV, a specific lysine tRNA is packaged in the virion and is required for HIV replication. Our laboratory has characterized the structural affects of several tRNA lysine anticodon modifications, and we have evaluated the thermodynamic effects of modification on RNA base-pairing. In addition to understanding the role of post-transcriptional modification on tRNA function, these studies have provided insight that suggest ways that natural modifications may have applications for modulating RNA recognition. We will present an overview of modification in the tRNA lysine anticodon, and summarize recent work on complexes of the tRNA with HIV viral RNA domains.