Knowledge of the dimensional changes occurring during electrochemical processes is fundamental for understanding of the electrochemical intercalation/insertion mechanism and for evaluation of potential application in electrochemical devices. We studied a highly oriented pyrolitic graphite (HOPG) electrode in perchloric acid, as a model to elucidate the mechanism of electrochemical anion intercalation in graphite. The aim of the work is the local and time dependent investigation of dimensional changes of the host material during electrochemical intercalation processes on the nanometer scale. We used atomic force microscopy (AFM), combined with cyclic voltammetry, as the in situ tool of analysis during intercalation and deintercalation of perchlorate anions. According to the AFM measurements, the HOPG interlayer spacing increases by 32% in agreement with the formation of stage IV of graphite intercalation compounds, when perchlorate anions intercalate. In addition, the local aspect of the process has been demonstrated by revealing coexisting regions with different kinetics for intercalation and deintercalation processes.