The study of chromosome structure with scanning probe microscopy provides a range of information from three-dimensional topographic structures through mechanical properties to optical information, usually fluorescence. For atomic force microscopy studies, the importance of removing cell debris from the chromosome surface has been recognized. Studies in aqueous environments reveal a highy swollen and tough chromosomal structure, but the charge interaction between the probe and specimen needs to be considered if high-resolution images are to be achieved. This charge interaction can be used to extract DNA strands of about 2 kbp from the chromosome. SPM studies of chromosomes may also be of value in the identification of defective chromosomes with either duplications or deletions.