The Agilent SurePrint G3 Human CGH+SNP microarrays allow for simultaneous analysis of chromosomal copy number changes and copy-neutral aberrations like loss of heterozygosity (LOH) and uniparental disomy (UPD) on the same array. The system allows researchers to study the genetic basis of developmental disorders as well as many cancers. To let researchers take advantage of the true power of the Agilent CGH+SNP and CGH microarrays, the CGH sample preparation has been automated by using the Agilent Bravo Automated Liquid Handling Platform. In this video we show the fragmentation, labeling, purification, and pre-hybridization setup in a 96-well format.