In the next generation of genome sequencing, sequence annotation plays an important role with respect to genome evaluation. The aim of annotation is to identify key features in the genome, such as genes and their products. Although annotation tools are available and some sequence features have been published, annotation information for many complete and partial genomes of Human T-Cell Lymphotropic Virus Type 1 (HTLV-1) remains unavailable from GenBank. Sequence analysis is critical to the understanding of the pathogenesis of HTLV-1, and a well-annotated reference sequence is an essential component in this analysis. More accurate and complete information about the HTLV-1 genome can assist the scientific community in investigations on possible therapeutic and prophylactic vaccines, as well as aid studies on the pathogenesis of HTLV-1-associated diseases. Here we describe for the first time the complete nucleotide position annotation of the frequently used HTLV-1 reference sequence, ATK1 (accession number: J02029.1).