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Ciprofloxacin (CFX) is an effective and relatively safe antimicrobial used in a variety of human infections. However, adverse drug reactions and positive results in genotoxic tests are reported. In order to understand the possible pathophysiological mechanisms of the toxic effects informed for CFX, lipid hydroperoxides (LOOH) -oxidative mediators of peroxidation- were quantified in liver and kidney of mice, after 15 to 360 minutes of the ciprofloxacin administration at doses of 10 mg/Kg or 100 mg/Kg by i.p. route. The peroxidation in the lipid fraction was evaluated by measuring the amount of hydroperoxides through the oxidation of 1-naphthyldiphenylphospine into its oxide and further quantification by high performance liquid chromatography. The initial content of lipid hydroperoxides (nmol/g tissue) was 253 +/- 3 in kidney and 143 +/- 12 in liver. CFX induced the maximal variation to 728 +/- 101 in kidney (P < 0.05) and 315 +/- 31 in liver (P < 0.01), after 15 min of 100 mg/Kg single dose. The variation in the LOOH levels was significant in kidney with both doses used and in liver after 100 mg/Kg until 60 min after the CFX administration, and then gradually fell to natural levels. The results demonstrated the effect of CFX on lipid oxidation, an indicator of oxidative effect. A natural protective capacity against this oxidation, more efficient in liver than in kidney, was observed.