The purpose of this work is to demonstrate a simple method that integrates custom DNA array synthesis and hybridization in a microfluidic channel. Commercial DLP projectors and a classical oligonucleotide synthesizer were integrated with a microfluidic chamber and constitute a Microfluidic ARray Synthesizer (MArS). Utilizing the benefit of microfluidics, the MArS produces two custom oligonucleotide arrays with reagent consumption for one array. The quality of the two arrays was examined by hybridization and shown to be almost identical. Post-synthesis deprotection of the array and hybridization performed in the same microfluidic chamber reduced overall DNA assay time by two orders. In addition, mismatch discrimination was enhanced using the microfluidic chamber. In summary, a simple method to build a custom array synthesizer is demonstrated and its performance is examined. Biotechnol. Bioeng. 2009;104: 400-407. (C) 2009 Wiley Periodicals, Inc.