Defects in graphene alter its electrical, chemical, magnetic and mechanical properties. The intentional creation of defects in graphene offers a means for engineering its properties. Techniques such as ion irradiation intentionally induce atomic defects in graphene, for example, divacancies, but these defects are randomly scattered over large distances. Control of defect formation with nanoscale precision remains a significant challenge. Here we show control over both the location and average complexity of defect formation in graphene by tailoring its exposure to a focussed electron beam. Divacancies and larger disordered structures are produced within a 10 × 10 nm(2) region of graphene and imaged after creation using an aberration-corrected transmission electron microscope. Some of the created defects were stable, whereas others relaxed to simpler structures through bond rotations and surface adatom incorporation. These results are important for the utilization of atomic defects in graphene-based research.