The resolution of scanning tunnelling microscopy (STM) and other scanning probe microscopies is unprecedented but the techniques are fraught with limitations as analytical tools. These limitations and their relationship to the physical mechanisms of image contrast are first discussed. Some new options based on in situ STM, which hold prospects for molecular- and mesoscopic-scale analytical chemistry, are then reviewed. They are illustrated by metallic electro-crystallisation and -dissolution, and in situ STM spectroscopy of large redox molecules. The biophysically oriented analytical options of in situ atomic force microscopy, and analytical chemical perspectives for the new microcantilever sensor techniques are also discussed.