Molecular analyses of early-stage prostate cancers are necessary to assesstheir potential clinical significance based on established and/or novel biomarkersfor tailored clinical management. A prerequisite for the application of RNA-basedanalyses of such, mostly macroscopically-undetectable, small prostate carcinomasis the recovery and preservation of sufficient RNA quantities and quality. Furthermore,in prostate cancer, heterogeneity is a common phenomenon that includes a juxtapositionof different tissue compositions and variable histological grades within the sametumor focus. To better understand the molecular mechanisms of prostate cancer,it is essential to correlate molecular data with a specific cell type. Here, wepresent a tissue collecting protocol which is aligned with the... preoperative evaluationof tumor localization. In combination with the technique of laser microdissectionand pressure catapulting, we are able to preserve RNA of high quality from homogeneouscell populations of macroscopically-undetectable small prostate carcinomas. Toobtain the necessary RNA quantities for whole genome cDNA microarrays, the isolatedtotal RNAs were amplified by T7-based RNA-polymerase in vitro transcription. Themicroarray analyses (Human Unigene Set RZPD3.1) resulted in 216 differentiallyexpressed genes (191 down-regulated, 25 up-regulated). Among these were severalknown prostate cancer relevant genes, such as AMACR, TARP, LIM, GPR160 (all up-regulated),CAV1, NTN1, MT1X; CLU, TRIM29, SPARCL1 and HSPB8 (all down-regulated).