The Ca(2+) channels ECaC1 and ECaC2 (TRPV5 and TRPV6) share several functional properties including permeation profile and Ca(2+)-dependent inactivation. However, the kinetics of ECaC2 currents notably differ from ECaC1 currents. The initial inactivation is much faster in ECaC2 than in ECaC1, and the kinetic differences between Ca(2+) and Ba(2+) currents are more pronounced for ECaC2 than ECaC1. Here, we identify the structural determinants for these functional differences. Chimeric proteins were expressed heterologously in HEK 293 cells and studied by patch clamp analysis. Both channels retained their phenotype after exchanging the complete N termini, the C termini, or even both N and C termini, i.e. ECaC1 with the ECaC2 N or C terminus still showed the ECaC1 phenotype and vice versa. The substitution of the intracellular loop between the transmembrane domains 2 and 3 of ECaC2 with that of ECaC1 induced a delay of inactivation. Three amino acid residues (Leu-409, Val-411 and Thr-412) present in this loop determine the fast inactivation behavior. When this intracellular loop between the transmembrane domains 2 and 3 of ECaC1 was exchanged with the TM2-TM3 loop of ECaC2, the ECaC1 kinetics were analogous to ECaC2. In conclusion, the TM2-TM3 loop is a critical determinant of the inactivation in ECaC1 and ECaC2.