The methylation-specific oligonucleotide (MSO) microarray is a high-throughput approach capable of detecting DNA methylation in genes across several CpG sites. Based on the bisulfite modification of DNA that converts unmethylated cytosines to uracil but leaves the 5'methylcytosine intact, the method utilizes short oligonucleotides corresponding to the methylated and unmethylated alleles as probes affixed on solid support and products amplified from bisulfite-treated DNA as targets for hybridization. MSO is suitable for examining a panel of genes across multiple clinical samples. This approach can generate a robust dataset for discovering profiles of gene methylation in cancer with aberrant DNA methylation in the neoplastic genome and widespread hypermethylation in tumor suppressor genes. MSO and other oligonucleotide-based arrays have been applied successfully for analyses of single genes and have been useful in delineating and predicting tumor subgroups using clustering methods. Here we focus on design criteria important to the interrogation of multiple CpG sites across several genes.