We have developed an integrated microarray production and analysis facility for quantitative comparisons of DNA copy number and RNA expression. The overall process is managed by a custom Oracle database that tracks clone acquisition and preparation of printing solutions, manages array printing and image acquisition, and stores results of the fluorescence analysis. The printing robot employs printing pins made from quartz capillary tubing with an outside diameter of approximately 0.4 mm, which has been heated and pulled to have an opening of approximately 25–50 µm. Each spot contains 50–100 pl of solution. Maximum load of a pin is restricted to approximately 0.2 µl, permitting thousands of spots to be printed from one load, and numerous print runs to be made from the same plates. Standard source plates contain 864 wells, so that a 16-pin print head prints arrays that are 12 mm2. The small diameter of the pins will permit printing out of 1,536 well plates, so that 36 pins could be used to print 13.5-mm arrays. Pin tip dimensions are being optimized to permit routine printing on less than 100-µm centers. The overall goal is to keep the array size small to minimize the amount of specimen material required for analysis, while employing a large number of printing pins to increase printing rate. The array-imaging system uses a CCD camera, allowing acquisition of 16-bit fluorescence data from the entire array with an exposure of several seconds or less for each fluorochrome. The custom-designed imaging lenses are chromatically corrected from 450 to 750 nm, and they provide flat images over the entire field. Illumination is supplied by a mercury arc lamp. Excitation and emission bands are established by computer-controlled filter wheels. Emission of at least four fluorochromes can be independently measured from a single specimen. These typically include DAPI, which is used as a counterstain to permit spot localization, and three labels in the specimen DNAs or RNAs, for example fluorescein, Cy3 and Cy5. Fluorescence ratios are calculated using custom software that automatically segments the spots of each sub array (the portion of the array printed by each pin) based on the DAPI image, determines local background and integrates signal intensities within each segmented spot. Our techniques permit measurement of genomic DNA copy number with ratio coefficient of variation of approximately 0.07 at the single-copy level, and measurement of expression levels with signal intensities approximately 100-fold lower than -actin (ratio coefficient of variation=0.1).