In order to investigate the prevalence of potential polymorphisms of the cathepsin W gene, the complete cDNA of 50 dyspeptic patients was analyzed. From those 37 (74%) revealed the wildtype sequence, 6 samples (12%) contained independent single base pair changes including 4 silent and 2 with amino acid changes. Furthermore, a triple-base pair polymorphism was found in 7 samples (14%, 4x heterozygous, 3x homozygous) leading to the following changes: F217S, H248Y, and I250T. Furthermore, a novel alternative splice variant concerning intron 10 was identified in 6 samples (12%). Notably, this novel isoform was only found in samples of gastric mucosa lymphocytes, whereas peripheral NK cells expressed cathepsin W wildtype only. Taken together, this study demonstrated for the fist time that a genetic variant and a novel isoform of cathepsin W are present in about 14% and 12%, respectively, within the Caucasian population. (C) 2004 Elsevier Inc. All rights reserved.