The nucleotide sequence of the human T-cell leukemia virus type II (HTLV-II) long terminal repeat (LTR) and its surrounding regions were determined. Our results show the following structural features: (i) the LTR is 763 base pairs (bp) in length and consists of 314 +/- 1 bp of region U3, 248 +/- 1 bp of region R, and 201 bp of region U5; (ii) the terminal nucleotides in the LTR form an inverted repeat of T-G.....C-A; (iii) 6-bp direct repeats of cellular sequences flanking the provirus were present; and (iv) the putative functional signals for initiation or termination of viral RNA synthesis were identified. Comparison of the HTLV-II LTR sequence with that previously published for adult T-cell leukemia virus (ATLV; HTLV-I) shows that the LTRs are distinct. Some small regions are conserved between HTLV-II and ATLV, involving sequences important for transcription and a sequence of 21 nucleotides repeated three times in U3. This 21-bp repeat may be important in regulating viral transcription in lymphoid cells.