Background HIV-1 integrase (IN) is an interesting target for the gene therapy of AIDS. Although the in vivo functions are not well characterized, it is thought that IN has pleiotropic effects and plays a central role in the interplay between the virus and the host cell. Expression of IN in mammalian cells has proven difficult. We have previously established a 293T-derived cell line that stably expresses high levels of HIV-1 IN from a synthetic gene. We now have constructed CEM-derived cell lines stably expressing the enzyme, or its different domains and studied the impact of IN expression on HIV-1 replication. Methods The CEM cell lines were selected following transduction with a retroviral vector encoding the full-length IN, the N-terminal domain, the, catalytic core or the C-terminal domain. Stable IN expression in CEM cell lines was verified by Western blotting. The impact of IN expression on HIV-1 replication and HIV-1 vector transduction was studied. Results A marked inhibitory effect on HIV-1 replication was observed in CEM cells expressing IN. Expression of IN interfered with both particle production and integration. Expression of the N-terminal domain alone was sufficient for the inhibiting of HIV-1 replication. Conclusions Expression of IN in CEM cells inhibits HIV-1 replication by a cumulative inhibitory effect on integration and particle production, in accord with the known pleiotropic interactions of IN. The inhibition of HIV-1 replication in CEM cells expressing the N-terminal domain of IN may lead to a novel approach for the gene therapy of AIDS. Copyright (C) 2004 John Wiley Sons, Ltd.