Microarrays are extensively used in molecular biology experiments. While several vendors offer microarrays on a variety of platforms, many researchers prefer to use custom microarrays with a selected list of clones for their experiments. Many research centers have established core facilities for the production of custom microarrays. Microarray production involves a number of steps, including maintaining a master list of stock clones, selecting required clones for custom microarrays, subculturing selected clones, amplifying inserts, recording results, and identifying the orientation of clones in the microarray. We have created a simple, user-friendly, and versatile Microsoft Excel spreadsheet-based software, Microarray Assistant, which can assist the user in all the steps of microarray design and synthesis. In addition, the program gives options to insert, delete, or interchange clones during various steps. The program also gives a visual picture of the locations of the clones in the plates, as well as in the microarray. The program can also be used to assist in the transfer of clones between plates of different configuration.