Cytochrome P450 aromatase is an essential enzyme for vertebrates. It is responsible for the conversion of androgens to estrogens in the brain and gonadal tissues. Aromatase converts testosterone into estradiol and therefore participates in the regulation of many processes which are controlled by estrogens such as development and fertility. Teleosts have been characterized as having exceptionally high levels of brain estrogen biosynthesis when compared to the brains of the other vertebrates. Little is known about the effects of estrogens on brain function in teleosts. The main objective of this study was to assess the effects of fadrozole, a powerful aromatase inhibitor, on gene expression in the zebrafish brain. To achieve this, male zebrafish were exposed to fadrozole for 10 days. This exposure causes a decrease in estrogens along with an increase in androgens. Plasma testosterone levels showed a 3-fold increase in response to the exposure. In the telencephalon, 235 genes were identified by Affymetrix GeneChip analysis as being differentially regulated. Real-time RT-PCR was used to validate the data obtained from the microarrays. This technique was also used to evaluate the response in the hypothalamus, which appears to follow similar transcriptional regulation. Gene ontology analysis of the microarray data revealed common biological processes and molecular functions such as sensory perception and detection of light stimulus, homeobox and transcription factor complexes. This study has identified genes which are directly and/or indirectly controlled by estrogens and androgens which helped to demonstrate the pronounced effects of endocrine disrupting chemicals on gene expression in the brain of teleosts. Collectively, the results provide a better understanding of the effects of aromatase inhibitors on gene expression and also shed light on the underlying effects of sex hormone variation and their importance in the brain of teleosts.