During the last decade, particle-induced X-ray emission spectrometry (PIXE) has been accepted by the analytical chemistry community as a standard method. Instead of routine bulk analysis of biomedical samples where several competing analytical techniques are available, the full strength of PIXE could be exploited in special applications where also location of the detected ions is desirable. In this article, two different approaches for this purpose are discussed and illustrated: (1) nuclear microscopy, where micro-PIXE utilizing a proton beam spot of approx 1 micron 2 or less promises unique perspectives to obtain elemental maps at the cellular level, and (2) in situ PIXE analysis of the minute metalloprotein volumes concentrated in thin-layer electrophoretograms.