Ca2+-ATPases on sarco (endo) plasmic reticulum and on plasma membrane are the representative members of P-type ATPase family and catalyze Ca2+ transport coupled with ATP hydrolysis, thereby play critical roles in Ca2+ homeostasis and cell functions. Their dysfunction by mutations and changes in expression levels result in various isoform-specific diseases. To understand molecular bases of the disruption of Ca2+ homeostasis and diseases, it is critically important to know how the Ca2+-ATPase functions, i.e. its structure-function relationship. In this manuscript, most recent atomic level-understanding of the Ca2+-ATPase and diseases caused by its defects will be reviewed.