Store-operated calcium entry relies on the formation of a specialized compartment derived from the endoplasmic reticulum (ER) and closely apposed to the plasma membrane. In this study, detailed ultrastructural analysis revealed the existence of three distinct structures derived from conventional ER: precortical ER, cortical ER, and thin cortical ER. Precortical subdomains of the ER enriched in STIM1 can form without contacting the plasma membrane. Upon ER calcium depletion, these subdomains are translocated to the plasma membrane to form cortical ER, which is still connected to the conventional ER. Thin cortical ER, depleted of BiP and deprived of attached ribosomes, may represent a specialized region dedicated to calcium regulation and not engaged in protein translocation and folding. These observations form the basis for future structure-function analysis of cortical ER.