The trichothecene deoxynivalenol (DON), a ribotoxic mycotoxin produced by toxigenic Fusarium sp. that commonly contaminates cereal-based foods, has the potential to adversely affect humans and animals and therefore represents an important public health concern (Pestka, 2010). Primary targets of this mycotoxin are monocytes and macrophages of the innate immune system. Both in vitro and in vivo studies have demonstrated that DON rapidly activates mitogen-activated protein kinases which drive upregulated expression of mRNAs and proteins for inflammation-related genes such as the cytokines, chemokines, and cyclooxygenase-2 (Chung et al., 2003; Islam et al., 2006; Moon and Pestka, 2002; Shifrin and Anderson, 1999; Zhou et al., 2003a). DON-induced increases in cellular pools of inflammation-associated mRNAs have been linked to both transcriptional activation and stabilization of mRNA through AUUUA motif in the 3′-untranslated region (UTR; Choi et al., 2009; Chung et al., 2003; Moon and Pestka, 2002) indicating that these two mechanisms contribute to upregulated gene expression. It is critical to note that the overall rate of translation in a cell depends not wholly on available mRNA but also on the capacity for and efficiency of translation (Proud, 2007; Sonenberg and Hinnebusch, 2009). Capacity relates to the availability and abundance of ribosomal subunits and other translational components, whereas efficiency is regulated by the rate of translational initiation and peptide chain elongation. Individual mRNAs are subject to additional levels of translational regulation, and elements in their 5′- and 3′-UTRs may interact with regulatory RNAs (e.g., antisense sequences and microRNAs) or RNA-binding proteins (RBPs) to modulate ribosomal association. As yet, it is not known whether ribotoxins such as DON might also selectively modulate translation through these mechanisms. In addition, DON’s capability of inhibiting translation at high concentrations (Zhou et al., 2003b) makes this question more complicated and interesting. One strategy for monitoring changes in protein expression in stressed cells is proteomic analysis, but such an approach is time-consuming, expensive, and relatively insensitive compared with transcriptomic approaches employing highly sensitive PCR (Cheeseman et al., 2011; Kuny et al., 2012). Additionally, measures of protein levels are affected by protein degradation and hence do not fully reflect translation. An alternative approach for identifying and quantitating genes being translated in cells under a specific set of conditions is to first isolate their polysomes and then profile the associated mRNAs. This “translatome” strategy has successfully been used in fungal, plant, and animal cells (Halbeisen and Gerber, 2009; Markou et al., 2010; Mustroph and Bailey-Serres, 2010; Preiss et al., 2003; Shenton et al., 2006). For example, yeasts exposed to different stresses, such as amino acid depletion and fusel alcohol addition, show distinct translational profiles (Smirnova et al., 2005), suggesting there is a role of translational regulation in rapidly responding environmental stress. Further studies employing additional high-throughput array analysis have revealed that translatome does not correlate with the transcriptome under mild stresses but does so under severe stresses such as amino acid deprivation (Halbeisen and Gerber, 2009), suggesting that coordination of translatome and transcriptome is stress dependent. Uncoupling of transcriptome and translatome has also been documented in human cells in response to various stimuli and stresses (Grolleau et al., 2002; Mikulits et al., 2000; Tebaldi et al., 2012). The purpose of this study was to test the hypothesis that DON selectively modulates translation of inflammation-associated genes in the RAW 264.7 murine macrophage cell model. Specifically, we employed a focused inflammation/autoimmune PCR array to compare the DON-induced inflammation-associated translatome and transcriptome. The results revealed that DON’s capacity to modulate translation of most inflammation-associated genes is predominantly driven by transcription and mRNA stabilization; however, a small subset of these genes appeared to be regulated, in part, by selective translation.