Microglial cells are the prime effectors in immune and inflammatory responses of the central nervous system (CNS). During pathological conditions, the activation of these cells helps restore CNS homeostasis. However, chronic microglial activation endangers neuronal survival through the release of various proinflammatory molecules and neurotoxins. Thus, negative regulators of microglial activation have been considered as potential therapeutic candidates to target neurodegeneration, such as that in Alzheimer's and Parkinson's diseases. Shikonin, a naphthoquinone pigment from the root of Lithospermum erythrorhizon, has long been used as an ointment for wound healing in traditional oriental medicine. Shikonin has been reported to have antibacterial, antitumor, and anti-inflammatory effects. The aim of this study was to examine whether shikonin represses microglial activation. In a study of shikonin and five of its derivatives, isobutyrylshikonin (IBS) and isovalerylshikonin (IVS) were the most effective at inhibiting LPS-induced nitric oxide (NO) release from microglial cells. Reverse transcriptase real-time PCR analysis revealed that pretreatment of rat brain microglia with IBS and IVS attenuated the LPS-induced expression of mRNAs encoding inducible NO synthase, tumor necrosis factor (TNF)-alpha, interleukin-1beta, and cyclooxygenase-2. In rat brain microglia, IBS and IVS reduced the LPS-stimulated production of TNF-alpha and prostaglandin E2. In addition, IBS and IVS significantly decreased LPS-induced IkappaB-alpha phosphorylation and NF-kappaB DNA binding activity, as well as the phosphorylation of the ERK1/2 and Akt signaling proteins. In organotypic hippocampal slice cultures, propidium iodide staining revealed prominent cell death in the hippocampal layer after 72h of LPS treatment. Both IBS and IVS clearly blocked the effect of LPS on hippocampal cell death and inhibited LPS-induced NO production in culture medium. These results suggest that IBS and IVS provide neuroprotection by reducing the release of various proinflammatory molecules from activated microglia.