Human T‐cell leukemia virus type 1 (HTLV‐1) is an oncogenic retrovirus; whereas HTLV‐1 mainly persists in the infected host cell as a provirus, it also causes a malignancy called adult T‐cell leukemia/lymphoma (ATLL) in about 5% of infection. HTLV‐1 replication is in most cases silent in vivo and viral de novo infection rarely occurs; HTLV‐1 rather relies on clonal proliferation of infected T cells for viral propagation as it multiplies the number of the provirus copies. It is mechanistically elusive how leukemic clones emerge during the course of HTLV‐1 infection in vivo and eventually cause the onset of ATLL. This review summarizes our current understanding of HTLV‐1 persistence and oncogenesis, with the incorporation of recent cutting‐edge discoveries obtained by high‐throughput sequencing.