BACKGROUND: Lipopolysaccharide (LPS) treatment of animals down-regulates the expression of hepatic genes involved in a broad variety of physiological processes, collectively known as the negative hepatic acute phase response (APR). Retinoid X receptor alpha (RXRalpha), the most highly expressed RXR isoform in liver, plays a central role in regulating bile acid, cholesterol, fatty acid, steroid and xenobiotic metabolism and homeostasis. Many of the genes regulated by RXRalpha are repressed during the negative hepatic APR, although the underlying mechanism is not known. We hypothesized that inflammation-induced alteration of the subcellular location of RXRalpha was a common mechanism underlying the negative hepatic APR. RESULTS: Nuclear RXRalpha protein levels were significantly reduced (~50%) within 1-2 hours after low-dose LPS treatment and remained so for at least 16 hours. RXRalpha was never detected in cytosolic extracts from saline-treated mice, yet was rapidly and profoundly detectable in the cytosol from 1 hour, to at least 4 hours, after LPS administration. These effects were specific, since the subcellular localization of the RXRalpha partner, the retinoic acid receptor (RARalpha), was unaffected by LPS. A potential cell-signaling modulator of RXRalpha activity, c-Jun-N-terminal kinase (JNK) was maximally activated at 1-2 hours, coincident with maximal levels of cytoplasmic RXRalpha. RNA levels of RXRalpha were unchanged, while expression of 6 sentinel hepatic genes regulated by RXRalpha were all markedly repressed after LPS treatment. This is likely due to reduced nuclear binding activities of regulatory RXRalpha-containing heterodimer pairs. CONCLUSION: The subcellular localization of native RXRalpha rapidly changes in response to LPS administration, correlating with induction of cell signaling pathways. This provides a novel and broad-ranging molecular mechanism for the suppression of RXRalpha-regulated genes in inflammation.