Pitx2, a bicoid-related homeobox gene, plays a crucial role in the left-right axis determination and dextral looping of the vertebrate developing heart. We have examined the differential expression and function of two Pitx2 isoforms (Pitx2a and Pitx2c) that differ in the region 5' to the homeodomain, in early chick embryogenesis. Northern blot and RT-PCR analyses indicated the existence of Pitx2a and Pitx2c but not Pitx2b in the developing chick embryos. In situ hybridization demonstrated a restricted expression of Pitx2c in the left lateral plate mesoderm (LPM), left half of heart tube and head mesoderm, but its absence in the extra-embryonic tissues where vasculogenesis occurs. RT-PCR experiments revealed that Pitx2a is absent in the left LPM, but is present in the head and extra-embryonic mesoderm. However, ectopic expression of either Pitx2c or Pitx2a via retroviral infection to the right LMP equally randomized heart looping direction. Mapping of the transcriptional activation function to the C terminus that is identical in both isoforms explained the similar results obtained by the gain-of-function approach. In contrast, elimination of Pitx2c expression from the left LMP by antisense oligonucleotide resulted in a randomization of heart looping, while treatment of embryos with antisense oligonucleotide specific to Pitx2a failed to generate similar effect. We further constructed RCAS retroviral vectors expressing dominant negative Pitx2 isoforms in which the C-terminal transcriptional activation domain was replaced by the repressor domain of the Drosophila Engrailed protein (En(r)). Ectopic expression of Pitx2c-En(r), but not Pitx2a-En(r), to the left LPM randomized the heart looping. The results thus demonstrate that Pitx2c plays a crucial role in the left-right axis determination and rightward heart looping during chick embryogenesis.