We describe a highly reproducible and multiplexed method, the GoldenGate assay for methylation, for high-throughput quantitative measurements of DNA methylation. It can analyze up to 1,536 targeted CpG sites in 96 samples simultaneously, using only 250 ng of genomic DNA. The method is akin to a “genotyping” of bisulfite-converted DNA. Assay probes can be designed to interrogate the Watson strand, the Crick strand, or both strands at each CpG site. Assay end products are processed using Illumina universal bead arrays. As a result, gene or CpG sets can be refined iteratively–-no custom arrays need to be developed. This method allows the detection of as little as 2.5% methylation, and can distinguish 17% difference in absolute methylation level between samples. The method is highly reproducible and compares very well with other common methods of methylation detection, such as methylation-specific PCR and bisulfite sequencing. The Illumina GoldenGate Methylation technology should prove useful for DNA methylation analyses in large populations, with potential application to biomarker discovery and validation.