The microphthalmia transcription factor (MITF) regulates different target genes in several distinct cell types, including osteoclasts. The role of the closely related factors TFE3 and TFEC in MITF action was studied. The TFE3 and TFEC proteins were expressed in osteoclast-like cells, and both could be immunoprecipitated in a complex with MITF. In transient transfection assays, TFE3 and TFEC could collaborate with MITF to superactivate the tartrate resistant acid phosphatase (TRAP) promoter, a target for MITF in osteoclasts. Although TFEC had been thought to act as a repressor, we could demonstrate that TFEC acted as a transactivator when fused to the gal4 DNA-binding domain in a yeast one-hybrid-type assay. Additionally, two mRNA isoforms of MITF, MITF-M and MITF-A, were detected in primary osteoclast-like cells by RT-PCR. In transient transfection assays, the MITF-A and MITF-M isoforms activated the promoter of the TRAP gene to the same extent, and both forms could collaborate equally well with TFE3 to activate the TRAP promoter. These results indicate that although different isoforms of MITF appear to be functionally similar, the TFE3 and TFEC proteins may collaborate with MITF to efficiently regulate expression of target genes in osteoclasts.