Recently scanning probe microscopy has made tremendous progress in imaging organic molecules with high lateral resolution. Atoms and bonds within individual molecules have been clearly resolved, indicating the exciting potential of this technique for studying molecular structures, bonding within and between molecules, molecular conformational changes and chemical reactions at the single-molecule level. It turns out that the key step enabling such studies is an atomically controlled functionalization of the microscope tip. In this Perspective, the different techniques used for high-resolution molecular imaging, their implementations, advantages and limitations are described, and possible scientific areas of applications are discussed. © 2011 Macmillan Publishers Limited. All rights reserved.