An assessment of developmental exposure to chemicals or complex mixtures of exogenous estrogenic chemicals, both natural and synthetic, requires a comprehensive understanding of their effects at the molecular, cellular and tissue level. To address these needs, a systematic approach was taken to assess the effects of male endocrine disruptors on reproductive development, spermatogenesis and testicular gene expression using cDNA microarrays. To develop a mouse testis cDNA microarray, a database of murine transcripts expressed in spermatogenesis and testis (dbTEST) was created to integrate publicly available literature, expression and EST sequencing data in a single curated and annotated source. From dbTEST, murine cDNA clones were selected, sequence verified, and used to construct a cDNA microarray containing approximately 2300 unique genes. Scanner output files are quantitated using Scanalyze (M. Eisen, http://rana.Stanford.EDU/software/). The resulting data files are processed using a PERL script which accepts user defined quality control parameters. This script performs background subtraction, normalization, spot flagging, calculates Cy5/Cy3 ratios, and annotates spot sequence and identity. The resulting expression and animal data are imported into an Oracle relational database that facilitates storage, analysis and retrieval of experimental information through SQL and PERL scripting. Input and customizable output of data is performed through an HTML interface for public and laboratory use.