autofluorescence from substances in cells often is at a level of brightness
one can live with.  IF level of fluorescence of fluorochrome labelled
antibody is BRIGHTER than the autofluorescence in these cells, you could
ignore autofluorescence.  We have done this recently and started to use
Alexa dyes from Molecular Probes, the Alexa 488 is a substitute for FITC,
is brighter, and also more stable (quenching by UV light is far less).  

Just another way to look to deal with autofluorescence 
 
Gayle Callis
MT,HT,HTL(ASCP)
Histopathology Supervisor
Veterinary Molecular Biology
Montana State University - Bozeman
Bozeman MT 59717-3610

406 994-6367
404 994-4303 (FAX)