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Production, usage and disposal of the munitions constituent (MC) cyclotrimethylenetrinitramine (RDX) has led to environmental releases on military facilities. The chemical attributes of RDX are conducive for leaching to surface water which may put aquatic organisms at risk of exposure. Because RDX has been observed to cause aberrant neuromuscular effects across a wide range of animal phyla, we assessed the effects of RDX on central nervous system (CNS) functions in the representative aquatic ecotoxicological model species, fathead minnow (Pimephales promelas). We developed a fathead minnow brain-tissue cDNA library enriched for transcripts differentially expressed in response to RDX and trinitrotoluene (TNT) exposure. All 4,128 cDNAs were sequenced, quality filtered and assembled yielding 2230 unique sequences and 945 significant blastx matches (E≤10−5). The cDNA library was leveraged to create custom-spotted microarrays for use in transcript expression assays. The impact of RDX on transcript expression in brain tissue was examined in fathead minnows exposed to RDX at 0.625, 2.5, 5, 10 mg/L or an acetone-spike control for 10 days. Overt toxicity of RDX in fathead minnow occurred only at the highest exposure concentration resulting in 50% mortality and weight loss. Conversely, Bayesian analysis of microarray data indicated significant changes in transcript expression at concentrations as low as 0.625 mg/L. In total, 154 cDNAs representing 44 unique transcripts were differentially expressed in RDX exposures, the majority of which were validated by reverse transcriptase-quantitative PCR (RT-qPCR). Investigation of molecular pathways, gene ontology (GO) and individual gene functions affected by RDX exposures indicated changes in metabolic processes involved in: oxygen transport, neurological function, calcium binding/signaling, energy metabolism, cell growth/division, oxidative stress and ubiquitination. In total, our study indicated that RDX exposure affected molecular processes critical to CNS function in fathead minnow.