Current advances in biomolecular technology allow precise genetic fingerprinting of specific cells responsible for the pathogenesis of human diseases. This study demonstrates the feasibility of enerating target samples from laser capture microdissection (LCM) tissues suitable for hybridization of high-density oligonucleotide arrays for gene expression profiling. RNA was successfully isolated by LCM from three paired specimens of oral cancer and linearly amplified using T7 RNA polymerase. Evaluation of the cDNA revealed that five of five cellular maintenance transcripts are detected. Biotinylated cRNA was generated and hybridized to the human Test 1 GeneChip "probe arrays, which demonstrated that the RNA is of sufficient quality and integrity to warrant further analysis. Subsequent hybridization of the samples to the HuGenFL GeneChip probe arrays revealed that 26.5%-33.0% of the approximately 7000 represented genes are expressed in each of the six samples. These results demonstrate that LCM-generated tissues can generate sufficient quality cRNA for high-density oligonucleotide microarray analysis, an important step in determining comprehensive gene expression profiling using this high-throughput technology.hybridization of LCM-generated RNA to cDNA-based expression microarrays, no report has yet shown the successful hybridization to high-density oligonucleotide mircoarrays. The limited quantity and quality of RNA isolated using LCM continues to be a technical obstacle for in vivo analysis of gene expression using microarrays. While RNA isolated from LCM-harvested tissue can be converted into cDNA libraries, it is generally agreed that the most accurate representation of gene expression for DNA chips is achieved by making the target sample directly from the RNA or by a T7-based linear RNA amplification (2,4,5). Comprehensive gene expression analysis of LCM-isolated pure cell populations will represent a major biomedical advance in our understanding of the pathogenesis of human disease (7). A major challenge in this line of investigation is the ability to generate a sufficient amount and quality of the desireddesired macromolecule from biopsied material. The GeneChip"probe arrays (Affymetrix, Santa Clara, CA, USA) allow the generation of accurate and reproducible mRNA transcript-level data (3,6,9). The HuGeneFL probe array contains probes representing approximately 7000 full-length human genes. The ability to generate target samples from LCM-based cells and tissues for hybridization to DNA chips represents an important advance that demonstrates the feasibility of using this method of sample collection for gene expression analysis on DNA chips.