To detect novel Wnt‐pathway genes involved in tumourigenesis, this study analysed the RNA expression levels of 40 genes of the Wnt pathway by chip hybridization of microdissected matched pairs of 54 primary prostate carcinomas. Eleven genes showed greater than two‐fold differential expression in at least 10% of prostate cancers. Three of these genes encode extracellular components of the Wnt pathway (WNT2, WIF1, SFRP4); two are receptors (FZD4, FZD6); two belong to the intracellular signal cascade (DVL1, PPP2CB); one regulates transcription (TCF4); and three represent genes regulated by this pathway (CCND2, CD44, MYC). While SFRP4, FZD4, FZD6, DVL1, TCF4, and MYC are up‐regulated, WIF1, WNT2, PPP2CB, CCND2, and CD44 are down‐regulated in certain prostate cancer patients. Wnt inhibitory factor 1 (WIF1) and secreted frizzled related protein (SFRP4) showed the most significant aberrant expression at the RNA level. WIF1 was down‐regulated in 64% of primary prostate cancers, while SFRP4 was up‐regulated in 81% of the patients. Immunohistochemical analysis using a polyclonal antibody revealed strong cytoplasmic perinuclear WIF1 expression in normal epithelial cells of the prostate, breast, lung, and urinary bladder. Strong reduction of WIF1 protein expression was found in 23% of prostate carcinomas, but also in 60% of breast, 75% of non‐small cell lung (NSCLC), and 26% of bladder cancers analysed. No significant association between WIF1 down‐regulation and tumour stage or grade was observed for prostate, breast or non‐small cell lung carcinomas, indicating that loss of WIF1 expression may be an early event in tumourigenesis in these tissues. However, down‐regulation of WIF1 correlated with higher tumour stage in urinary bladder tumours (pTa versus pT1–pT4; p = 0.038). Copyright © 2003 John Wiley & Sons, Ltd.