The completion of the Human Genome Project and the emergence of high-throughput technologies at the dawn of the new millennium, are rapidly changing the way we approach biological problems. DNA microarrays represent a promising new technological development, widely used for the investigation and identification of genes associated with important biological processes. The chapter is divided in two parts: the first discusses current methods for the acquisition and quantitation of the microarray image while the second focuses in the analysis and interpretation of the microarray signals (standardization, normalization, statistical analysis etc.)