The endoplasmic reticulum (ER) and mitochondria accumulate Ca(2+) within their lumens to regulate numerous cell functions. However, determining the dynamics of intraorganellar Ca(2+) has proven to be difficult. Here we describe a family of genetically encoded Ca(2+) indicators, named calcium-measuring organelle-entrapped protein indicators (CEPIA), which can be utilized for intraorganellar Ca(2+) imaging. CEPIA, which emit green, red or blue/green fluorescence, are engineered to bind Ca(2+) at intraorganellar Ca(2+) concentrations. They can be targeted to different organelles and may be used alongside other fluorescent molecular markers, expanding the range of cell functions that can be simultaneously analysed. The spatiotemporal resolution of CEPIA makes it possible to resolve Ca(2+) import into individual mitochondria while simultaneously measuring ER and cytosolic Ca(2+). We have used these imaging capabilities to reveal differential Ca(2+) handling in individual mitochondria. CEPIA imaging is a useful new tool to further the understanding of organellar functions.