DNA aptamers are versatile recognition elements for pharmaceutical, diagnostic, and life science applications. Identification and optimization of the minimal functional sequence after aptamer selection is a bottleneck for developing aptamer applications. DNA microarray technology proved a facile means for screening thousands of aptamer sequence permutations to identify functional aptamer domains. This chapter describes the detailed methodology for designing aptamer arrays to identify minimal aptamer binding domains as well as elucidating the relationship between aptamer structure and function, using immunoglobulin E as a model protein.