Work in the DeRisi lab has recently established that the only essential apicoplast metabolic function during asexual blood phase growth is isoprenoid synthesis (Yeh and DeRisi, PLoS Biol. 2011). Cultures supplemented with the sole essential metabolic output of this pathway, isopentenyl pyrophosphate (IPP), are completely resistant to antibiotic treatment and moreover, they continue to grow and propagate indefinitely even though these parasites are devoid of the apicoplast genome and organelle (apicoplast(-)). Thus, rescue with IPP provides an unique opportunity to determine whether the specific action of anti-malarial compound is targeted at the apicoplast. The DeRisi lab screened the MMV Malaria Box set of 400 anti-malarial compounds using the W2 strain in a 72 hr growth assay monitored by flow cytometry both in the presence and absence of supplemental IPP. Here, we report the raw screening data for growth in both conditions when treated with 5uM of each Malaria Box compound.