Microarray technology provides efficient access to genetic information using miniaturized, high-density arrays of DNA probes. We investigated the application of luminescent nanoparticles as probes for Affymetrix GeneChips detection without the need for signal amplification. Our goal is to investigate the feasibility of using luminescent nanoparticles as probes in a commercial microarray system without changing its configurations. With the present imaging modality and existing optical excitation and detection systems of the Affymetrix GeneChips, our early results indicate that nanoparticles not only can be used for GeneChip labeling but also are superior to the traditional fluorescent protein streptavidin-phycoerythrin (SAPE). The advantage of the particles lies in a simplified staining procedure, higher photobleaching threshold, and enhanced luminescence signal. The nanoparticles can be used for detection of low-abundance targets without any amplification step. A concentration detection limit of 50 fM has been achieved. This work demonstrates the feasibility of using luminescent nanoparticles as probes for commercial microarray systems, making them less costly, more reproducible, and potentially quantitative.