MoS2 single layers have recently emerged as strong competitors of graphene in electronic and optoelectronic device applications due to their intrinsic direct bandgap. However, transport measurements reveal the crucial role of defect-induced electronic states, pointing out the fundamental importance of characterizing their intrinsic defect structure. Transmission Electron Microscopy (TEM) is able to image atomic scale defects in MoS2 single layers, but the imaged defect structure is far from the one probed in the electronic devices, as the defect density and distribution are substantially altered during the TEM imaging. Here, we report that under special imaging conditions, STM measurements can fully resolve the native atomic scale defect structure of MoS2 single layers. Our STM investigations clearly resolve a high intrinsic concentration of individual sulfur atom vacancies, and experimentally identify the nature of the defect induced electronic mid-gap states, by combining topographic STM images with ab intio calculations. Experimental data on the intrinsic defect structure and the associated defect-bound electronic states that can be directly used for the interpretation of transport measurements are essential to fully understand the operation, reliability and performance limitations of realistic electronic devices based on MoS2 single layers.