Stromal interaction molecule 1 (STIM1) is an endoplasmic reticulum (ER)-membrane associated Ca(2+) sensor which activates store-operated Ca(2+) entry (SOCE). The homologue, STIM2 possesses a high sequence identity to STIM1 ( approximately 61%), while its role in SOCE seems to be distinct from that of STIM1. In order to understand the underlying mechanism for the functional differences between STIM1 and STIM2, we investigated the biophysical properties of the luminal Ca(2+)-binding region which contains an EF-hand motif and a sterile alpha-motif (SAM) domain (hereafter called EF-SAM; residues 58-201 in STIM1 and 149-292 in STIM2). STIM2 EF-SAM has a low apparent Ca(2+)-binding affinity (K(d) approximately 0.5mM), which is similar to that reported for STIM1 EF-SAM. In the presence of Ca(2+), STIM2 EF-SAM is monomeric and well-folded, analogous to what was previously observed for STIM1 EF-SAM. In contrast to apo STIM1 EF-SAM, apo STIM2 EF-SAM is more structurally stable and does not readily aggregate. Our circular dichroism (CD) data demonstrate the existence of a long-lived, well-folded monomeric state for apo STIM2 EF-SAM, together with a less alpha-helical/partially unfolded aggregated state which is detectable only at higher protein concentrations and higher temperatures. Our biophysical studies reveal a structural stability difference in the EF-SAM region between STIM1 and STIM2, which may account for their different biological functions.