With the commercial availability of genome tiling microarrays, many researchers have dabbled in conducting ChIP-chip to study the genome-wide interaction between trans-factors and cis-elements. However, the ChIP-chip technique is tricky to master, and its downstream analysis is challenging. For the second Cistrome meeting, we will have a preconference workshop to trouble-shoot technical aspects of ChIP-chip, and the main conference to exchange scientific insights and experiences in our ChIP-chip applications.