As more and more genetically modified organisms (GMO) are commercialized, efficient and inexpensive assays are required for their quick detection. An event-specific detection strategy based on the unique and specific sequences of integration junctions is useful because of its high specificity. This study developed a system for detecting six GM maize lines (Bt11, Bt176, GA21, MON810, NK603, and T25) using optical silicon thin-film biosensor chips. Aldehyde-labeled probes were arrayed and covalently attached to a hydrazine-derivatized chip surface. Biotinylated PCR amplicons were then hybridized with the probes. After washing and brief incubation with an anti-biotin IgG horseradish peroxidase conjugate and a precipitable horseradish peroxidase substrate, biotinylated PCR amplicons perfectly matched with the probes can be visualized by the color change on the chip surface (gold to blue/purple). This assay is extremely robust, exhibits high sensitivity and specificity, and is flexible from low through moderate to high throughput.