At the heart of modern oxide chemistry lies the recognition that beneficial ( as well as deleterious) materials properties can be obtained by deliberate deviations of oxygen atom occupancy from the ideal stoichiometry(1,2). Conversely, the capability to control and confine oxygen vacancies will be important to realize the full potential of perovskite ferroelectric materials, varistors and field-effect devices(3,4). In transition metal oxides, oxygen vacancies are generally electron donors, and in strontium titanate (SrTiO3) thin films, oxygen vacancies ( unlike impurity dopants) are particularly important because they tend to retain high carrier mobilities, even at high carrier densities(5). Here we report the successful fabrication, using a pulsed laser deposition technique, of SrTiO3 superlattice films with oxygen doping profiles that exhibit subnanometre abruptness. We profile the vacancy concentrations on an atomic scale using annular-dark-field electron microscopy and core-level spectroscopy, and demonstrate absolute detection sensitivities of one to four oxygen vacancies. Our findings open a pathway to the microscopic study of individual vacancies and their clustering, not only in oxides, but in crystalline materials more generally.