CaT1, the calcium transport protein 1 encoded by TRPV6, is able to generate a Ca2+ conductance similar but not identical to the classical CRAC current in mucosal-type mast cells. Here we show that CaT1-derived Ca2+ entry into HEK293 cells is effectively inhibited by either expression of various dominant negative N-terminal fragments of CaT1 (N334-CaT1, N198-CaT1 and N154-CaT1) or by antisense suppression. By contrast, the endogenous CRAC current of the mast cells was unaffected by CaT1 antisense and siRNA knockdown but markedly suppressed by two (N334-CaT1, N198-CaT1) of the dominant negative N-CaT1 fragments. Inhibition of CRAC current was not an unspecific, toxic effect, as inward rectifier K+ and MagNuM currents of the mast cells were not significantly affected by these N-CaT1 fragments. The shortest N154-CaT1 fragment inhibited CaT1-derived currents in mast cells, however, failed to inhibit CRAC currents. Thus, the structural requirements of rCaT N-terminal fragments for inhibition of rCaT1 and CRAC channels are divergent. These results together with the lack of CaT1 antisense and siRNA effects on currents render it unlikely that CaT1 is a component of native CRAC channels in mast cells. The data further demonstrate a novel strategy for CRAC current inhibition by a N-terminal structure of CaT1.