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Human babesiosis is a global emerging infectious disease caused by intraerythrocytic parasites of the genus Babesia. Its biology has remained largely unexplored due to a lack of critical tools and techniques required to define the various stages and phases of the parasite's cycle in its host RBC and the interplay between host and parasite. This article presents a powerful set of tools combining stage synchronization of the parasite with a platform that encompasses both a flow cytometric evaluation of the subpopulation structure of the parasite population together with a morphological assessment of the population parasites using light microscopy of conventional Giemsa stained smears. Together, these yield specific information on the effect of any drug/condition of interest and its targeted biological process, allowing the characterization of the adaptive response of parasites to a particular stressor agent. Three inhibitors were used in this study, each targeting a specific phase of the parasite's lifecycle, neuraminidase for host cell invasion, N-acetyl-L-leucyl-L-leucyl-L-norleucinal for parasite development and EGTA for parasite egress from the host cell. Results presented prove the power of this combination platform in discriminating the specific targets among the life-cycle processes of the parasite-invasion, development/proliferation and egress. This will expand the range of queries that can now be successfully addressed in this parasite, opening avenues for the development of new methods to control babesiosis, either by chemicals (screening for new chemotherapy drugs or defining levels of parasite resistance) or physical methods (light irradiation or heat shock used in pathogen reduction/elimination methods). © 2017 International Society for Advancement of Cytometry.