To facilitate the molecular analysis of tissues in adult zebrafish, we tested eight different fixation and decalcification conditions for the ability to yield DNA suitable for PCR and tissue immunoreactivity, following paraffin embedding and sectioning. Although all conditions resulted in good tissue histology and immunocytochemistry, only two conditions left the DNA intact as seen by PCR. The results indicate that zebrafish fixed in either 10% neutral buffered formalin or 4% paraformaldehyde, followed by decalcification in 0.5 M EDTA, is an easy and reliable method that allows molecular experiments and histology to be performed on the same specimen. The fixation and decalcification by Dietrich's solution permitted the PCR amplification of DNA fragments of 250 but not 1000 bp. Therefore, a protocol of formalin or paraformaldehyde fixation followed by decalcification with EDTA is broadly applicable to a variety of vertebrate tissues when excellent histological, immunocytochemical, and genotypic analyses may be simultaneously required.