Metal oxides are abundant in nature and they are some of the most versatile materials for applications ranging from catalysis to novel electronics. The physical and chemical properties of metal oxides are dramatically influenced, and can be judiciously tailored, by defects. Small changes in stoichiometry introduce so-called intrinsic defects, e.g., atomic vacancies and/or interstitials. This review gives an overview of using Scanning Probe Microscopy (SPM), in particular Scanning Tunneling Microscopy (STM), to study the changes in the local geometric and electronic structure related to these intrinsic point defects at the surfaces of metal oxides. Three prototypical systems are discussed: titanium dioxide (TiO), iron oxides (FeO), and, as an example for a post-transition-metal oxide, indium oxide (InO). Each of these three materials prefers a different type of surface point defect: oxygen vacancies, cation vacancies, and cation adatoms, respectively. The different modes of STM imaging and the promising capabilities of non-contact Atomic Force Microscopy (nc-AFM) techniques are discussed, as well as the capability of STM to manipulate single point defects.