The detection of bromine in human metaphase chromosomes labelled with the thymidine-analog BrdU, by imaging Secondary Ion Mass Spectrometry (SIMS) with a high resolution scanning ion microprobe, provides detailed maps of the AT distribution within the chromosomes. Similarly, maps of the emitted CN-molecular ions describe the overall DNA, RNA and protein distribution, details of which are also revealed by maps of the divalent cations Ca+ and Mg+. Base-specific banding patterns (SIMS bands), mimicking the well known G-or Q-bands resulting from conventional staining methods for optical microscopy, are observed in several preparations, more noticeably in mitotic cells at the first cell division, after in situ DNA denaturation, or Giemsa staining. A structured distribution, seemingly related to G/Q-banding patterns, is also observed in the Mg+ and Ca+ maps. The differential label signal intensities between sister chromatids, at the second cell division and beyond, manifest the occurrence of sister chromatid exchanges (SCE), occurring both spontaneously and induced following exposure of the cells to the chemical aphidicolin (an inhibitor of DNA replication). Imaging SIMS emerges as a powerful investigative method for the study of chromosome structure and the elucidation of banding mechanisms, to assess the removal of proteins and DNA involved in chromosome preparation and in situ procedures, and in the study of a number of cytogenetic phenomena.