Atomic force microscopy (AFM) can dynamically detect the adhesion or affinity force between a sample surface and a cantilever. This feature is useful as a detection method using aptamers - single-strand DNA that recognizes its target with very high affinity. The present study proposes a novel DNA aptamer-based sensing system using AFM. In this study, thrombin was chosen as the target molecule, and a DNA aptamer-based AFM sensing system based on competition was developed. The affinity force between the gold chip and the cantilever decreased as the concentration of thrombin increased. Moreover, a low detection limit of 0.2 nM was achieved. Therefore, the AFM sensing system used would be appropriate for the measurement of various chemical compounds. (C) 2011, The Society for Biotechnology, Japan. All rights reserved.