High-density, spatially addressable arrays of DNA probes offer a high-throughput approach to DNA sequence analysis that is likely to have a major impact on biological and genetic research. These arrays are comprised of short strands of immobilized DNA (“probe”) sequences prepared synthetically on a planar glass support. Samples of unknown, fluorescentlylabeled strands of “target' DNA can be analyzed by sequence-specific binding (“hybridization”) to the arrays in order to extract detailed sequence information. The detection sensitivity of these arrays is dependent on quantity and density of immobilized probe molecules on the surface, as well as the thermodynamics of nucleic acid hybridization. In this report, substrates with a porous, “3-dimensional” surface layer were investigated as a means of increasing the number of available probes, and therefore the amount of detectable bound target per unit area. Two methods for creating porous silica layers were investigated - a “subtractive” method and an “additive” method. For the systems investigated, the additive method, sol-gel processing, offered the most promising route for high density DNA arrays.