The objective of this study was to identify transcription factors associated with differentiation of the chorionic girdle, the invasive form of equine trophoblast. The expression patterns of five transcription factors were determined on a panel of conceptus tissues from early horse pregnancy. Tissues from Days 15 through 46 were tested. Eomesodermin (EOMES), glial cells missing homologue 1 (GCM1), heart and neural crest derivatives expressed transcript 1 (HAND1), caudal type homeobox 2 (CDX2), and distal-less homeobox 3 (DLX3) were detected in horse trophoblast, but the expression patterns for these genes varied. EOMES had the most restricted distribution, while DLX3 CDX2, and HAND1 were widely expressed. GCM1 seemed to increase in the developing chorionic girdle, and this was confirmed by quantitative RT-PCR assays. GCM1 expression preceded a striking increase in expression of equine chorionic gonadotropin beta (CGB) in the chorionic girdle, and binding sites for GCM1 were discovered in the promoter region of the CGB gene. GCM1, CGB, and CGA mRNA were expressed preferentially in binucleate cells as opposed to uninucleate cells of the chorionic girdle. Based on these findings, it is likely that GCM1 has a role in differentiation and function of the invasive trophoblast of the equine chorionic girdle and endometrial cups. The equine binucleate chorionic girdle (CG) secreting trophoblast shares molecular, morphological, and functional characteristics with human syncytiotrophoblast and represents a model for studies of human placental function.