It is now becoming generally recognized that microarray technology will be a fundamental tool used in future genomics research. As the technology becomes more widely accessible, larger numbers of biologists will be able to shift their focus from the study of individual events to the analysis of complex systems and pathways. To help drive this transition, we have used novel tools for creating and reading high-density microarrays of spotted DNAs to investigate whether conventional chemistries (for example, Southern, northern and western blots) might be applied to microarray analysis. It had previously been assumed that these well-documented methodologies could not be used for microarray analysis because: (i) spotting instruments could not produce arrays on membranes such as nitrocellulose or nylon; and (ii) these membranes were thought to produce levels of fluorescence which would make analysis impossible. We will show data developed using a Pin-and-Ring™ spotting system (the GMS 417 Arrayer) and an epi-fluorescent confocal laser microscope that employs Flying Objective™ scanning technology (the GMS 418 Array Scanner), demonstrating that conventional chemistries can be used for microarray analysis. We believe that demonstration of the feasibility of this approach will facilitate the migration of more biologists toward the use of microarray technology, as they will now be able to use commercially available instrumentation and familiar methodologies for highly parallel genomic analysis. These novel instrument systems also provide enhanced performance (for example, consistency of spotting, speed and sensitivity of scanning) with biochemical methodologies developed specifically for microarray analysis, so that scientists can obtain the same degree of analytical power independent of the biochemistry they choose to employ.