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Oxysterols are oxidised forms of cholesterol or its precursors. In this article we will concentrate specifically on those formed in mammalian systems. Oxidation may be catalysed by endogenous enzymes or through reactive oxygen species forming a myriad of potential products. A number of these products are biologically active, and oxysterols may have roles in cholesterol homeostasis, neurogenesis, protein prenylation and in the immune system. Oxysterols are also implicated in aetiology of disease states including atherosclerosis, neurodegenerative and inflammatory diseases. Reports indicating the levels of oxysterols in plasma, cerebrospinal fluid and various tissues are in many cases unrealistic owing to a lack of attention to the possibility of autoxidation, a process by which oxysterols are formed from cholesterol by oxygen in air. This article comprises a critical assessment of the technical difficulties of oxysterol analysis, highlights methodologies utilising best practise and discusses newer procedures.