This document from Wright Cell Imaging Facility, Toronto Western Research Institute, is a summary of information from the Confocal listserver archives, Cytometry Archives and the Histonet archives.

"What we most often mean by “autofluorescence” is “natural fluorescence” or “fixative-induced fluorescence”. The emission spectra of natural fluorescence and fixation-induced fluorescence is very broad compared to the spectra of the dyes, probes and proteins we are interested in, making it difficult to separated wanted from unwanted fluorescence by traditional filtering methods"