The use of nanoparticles is one of the fastest expanding fields in industrial as well as in medical applications, owing to their remarkable characteristics. Silver nanoparticles (AgNPs) are among the most-commercialized nanoparticles because of their antibacterial effects. Laser postionization secondary neutral mass spectrometry (laser-SNMS) and time-of-flight secondary ion mass spectrometry in combination with argon cluster ion sputtering was used for the first time to investigate the effects of AgNPs on Madin-Darby canine kidney (MDCK) II cells. Depth profiles and high-resolution three dimensional (3D) images of nanoparticles and organic compounds from cells were obtained using an Ar cluster ion beam for sputtering and Bi3 (+) primary ions for the analysis. The 3D distribution of AgNPs and other organic compounds in MDCK II cells could be readily detected with very high efficiency, sensitivity, and submicron lateral resolution. The argon cluster ion beam is well suited for the sputtering of biological samples. It enables a high sample removal rate along with low molecular degradation. The outer membrane, the cytoplasm, and the nuclei of the cells could be clearly visualized using the signals PO(+) and C3H8N(+) or CN(+) and C3H8N(+). The laser-SNMS images showed unambiguously that AgNPs are incorporated by MDCK II cells and often form silver aggregates with a diameter of a few micrometers, mainly close to the outside of the cell nuclei.