In dynamic environments, intracellular homeostasis is maintained by transport systems found in all cells. While bacterial influx systems for essential trace cations are known to contribute to pathogenesis, efflux systems have been characterized mainly in contaminated environmental sites. We describe that the high calcium concentrations in the normal human host were toxic to pneumococci and that bacterial survival in vivo depended on CaxP, the first Ca2+ exporter reported in bacteria. CaxP homologues were found in the eukaryotic sacroplasmic reticulum and in many bacterial genomes. A caxP− mutant accumulated intracellular calcium, a state that was used to reveal signalling networks responsive to changes in intracellular calcium concentration. Chemical inhibition of CaxP was bacteriostatic in physiological calcium concentrations, suggesting a new antibiotic target uncovered under conditions in the eukaryotic host.