Transition-metal perovskite oxides exhibit a wide range of extraordinary but imperfectly understood phenomena. The best known examples are high-temperature superconductivity in copper oxides(1), and colossal magnetoresistance in manganese oxides ('manganites')(2,3). All of these materials undergo a range of order-disorder transitions associated with changes in charge, spin, orbital and lattice degrees of freedom. Measurements of such order are usually made by diffraction techniques, which detect the ionic cores and the spins of the conduction electrons. Unfortunately, because such techniques are only weakly sensitive to valence electrons and yield superpositions of signals from distinct submicrometre-scale phases, they cannot directly image phase coexistence and charge ordering, two key features of the manganites. Here we present scanning tunnelling microscope measurements of the manganite Bi1- xCaxMnO3. We show that charge ordering and phase separation can be resolved in real space with atomic-scale resolution. By taking together images and current-voltage spectroscopy data we find that charge order correlates with both structural order and the local conductive state (either metallic or insulating). These experiments provide an atomic-scale basis for descriptions(4) of manganites as mixtures of electronically and structurally distinct phases.