The seed oil of Carapa guianensis (Aublet), a tree from the Meliaceae family commonly known as andiroba, is widely used in Brazilian traditional medicine because of its multiple curative properties against fever and rheumatism and as an anti-inflammatory agent, antibacterial agent, and insect repellant. Since there is no consensus on the best way to obtain the C. guianensis oil and due to its ethnomedicinal properties, the aim of the present research was to evaluate the chemical composition, free-radical scavenging activity, and mutagenic and genotoxicity properties of three C. guianensis oils obtained by different extraction methods. The phenolic contents were evaluated by spectrophotometry. Oil 1 was obtained by pressing the dried seeds at room temperature; oil 2 was obtained by autoclaving, drying, and pressing; oil 3 was obtained by Soxhlet extraction at 30-60°C using petroleum ether. The oil from each process presented differential yields, physicochemical properties, and phenolic contents. Oil 1 showed a higher scavenging activity against the DPPH radical when compared to oils 2 and 3, suggesting a significant antioxidant activity. All oils were shown to be cytotoxic to bacteria and to CHO-K1 and RAW264.7 cells. At noncytotoxic concentrations, oil 2 presented mutagenicity to Salmonella enterica serovar Typhimurium and induced micronuclei in both cell types. Under the same conditions, oil 3 also induced micronucleus formation. However, the present data demonstrated that oil 1, extracted without using high temperatures, was the safest for use as compared to the other two oils, not showing mutagenicity or micronucleus induction.