To examine the possibility that ETS family transcription factors, PU.1, SPI-B, ELF-1, ERG-3, ETS-1 and TEL, and homeodomain proteins, HOXA10, HOXC13, MEIS1 and PBX1B, function cooperatively, we investigated their interactions. In luciferase assays, HOXA10 and HOXC13 augmented the activity of PU.1 and SPI-B while diminishing that of ELF-1 and ERG-3. MEIS1 diminished the activity of ETS-1. No clear effects were observed for other combinations. Immunoprecipitation assays showed protein-protein interactions among the combinations exhibiting functional interactions. A mutation of HOXC13, which abolished binding to ELF-1, also abolished the diminishing effect on ELF-1. The results suggest functional interaction through physical interactions.