Fluorescence microscopy is an important method in mycology. It is a co
mmon procedure used in immunology or histology and more recently in mo
dern techniques of molecular biology like in-situ hybridization. Since
several molds and yeasts show autofluorescence, an interference of th
is phenomenon with the detection method cannot be excluded. Therefore,
we studied autofluorescence in fungi in more detail, in particular wi
th respect to the dependence of this phenomenon from growth conditions
, fixing method or mounting medium used. Here we show that moulds cult
ivated in a liquid medium are strongly autofluorescent which could be
considerably reduced by repetitive washing. In moulds, we did not find
important differences in autofluorescence levels with the three fixin
g methods under study. However, this finding cannot be generalized. Th
us, in the yeast Candida albicans we found the autofluorescence patter
n being largely dependent from the fixing method and the excitation wa
ve length, respectively. In particular, with green excitation we could
show that aceton fixation resulted in strong fluorescence of individu
al cells within a vast population of cells showing little or no autofl
uorescence. In addition, we could demonstrate that mounting media are
able to strongly modify autofluorescence in fungi. Using digital image
acquisition with a cooled CCD camera we were able to quantify the inf
luence of different mounting media on fluorescence intensities of Aspe
rgillus fumigatus. Diagnostic methods in mycology based on fluorescenc
e microscopy have to be thoroughly evaluated in order to prevent false
positive results due to fungal autofluorescence.