An increased level of cytosolic free calcium (Ca(2+)) is an essential second messenger for apical organelle discharge in Plasmodium falciparum merozoites. Here, we describe a method for isolation of viable and invasive P. falciparum merozoites. We also describe methods to measure cytosolic Ca(2+) levels in merozoites using fluorescent intracellular calcium indicators such as Fluo-4AM by flow cytometry. Further, we also describe a flow cytometry-based method to detect translocation of apical organelle proteins to the surface of merozoites. Using these methods, we have advanced our understanding of signaling pathways involved in apical organelle discharge during erythrocyte invasion by P. falciparum merozoites.