Cultures of Plasmodium falciparum often contain a heterogeneous parasite population. However, several studies require analysis of single infected erythrocytes (IEs) or a clonal parasite population derived from a single parasite. This protocol describes an efficient method for cloning by using fluorescence-activated cell sorting (FACS). For this, an antibody for a particular IEs surface protein it is added to the cell mixture to separate positive and negative IEs for that marker. After the separation, the viable homogeneous population can be used to grow in culture or for molecular analysis.