Using hematoxylin and eosin (H&E)-stained sections, Paneth cells are identified by the presence of eosinophilic granules. Several other methods have been proposed to stain Paneth cells. Recently, we noticed that Paneth cells were autofluorescent in H&E sections. To assess the number of Paneth cells by this method, 30 surgical specimens from the small bowel and 10 from the colon with IBD were investigated. Consecutive sections were stained with H&E and immunostained with lysozyme (Lz). Paneth cell counting was done in 20 well-oriented, vertically cut crypts per-case using alternatively transmitted light (TL) and incident-light fluorescence (ILF). When H&E and Lz sections were observed with TL, the number of Paneth cells was easily assessed in some crypts, but in crypts having numerous Paneth cells, their exact number was ascertainable. On the other hand, using IFL, the number of H&E-stained Paneth cells-crypt was easily assessed, even in crypts with Paneth cell clustering. Using H&E-ILF, a mean of 3.9 (range 3-8) Paneth cells-pe-crypt was found in the normal small bowel and a mean of 3.3 (range 1-14) in the colon with IBD. ILF provided the adequate visual conditions--i.e. a dark, non-autofluorescent background--for assessing the actual number of normal and metaplastic Paneth cells, even when arranged in tight cell groups. The present method will improve the enumeration of the actual number of normal and metaplastic Paneth cells both in experimental research and in clinical trials.