Bixin is the most used carothenoid in food industry. It is conventionally extracted from annatto seeds (Bixa orellana L.) by alkaline solutions or organic solvents, producing bixin with low purity and generating toxic waste. This study aimed to compare different clean technologies for extraction of nutraceuticals (bixin and tocols) from annatto seeds, using a fixed bed extractor. The solvents used were supercritical CO2, ethanol and a mixture of ethanol and water. Conventional extractions using water and chloroform were also conducted, for comparison. Scanning electron microscopy was used to evaluate the surface of seeds and confirm experimental results. The best extraction efficiencies (for bixin) were using ethanol (ambient pressure) and a sequential extraction (supercritical CO2 as pretreatment followed by ethanol). This last result has also shown a good recovery of delta-tocotrienol, a powerful natural antioxidaht. Higher concentrations of bixin in extracts were obtained using pure ethanol at ambient and high pressures. (C) 2015 Elsevier B.V. All rights reserved.