Selenium deficiency could be expected to lead to enhanced lipid peroxidation through loss of selenium-dependent glutathione peroxidase activity. Such a relation has, however, been difficult to verify. In the present study, the influence of selenium deficiency in rats on in vivo doses of some endogenously occurring low-molecular mass aldehydes and epoxides was determined. In vivo doses were measured by mass-spectrometric analysis according the N-alkyl Edman method of reaction products (adducts) with N-terminal valines in hemoglobin. Despite variations between experiments, the adduct levels of acetaldehyde and malonaldehyde were shown to be significantly higher in rats fed a selenium-deficient diet than in controls fed a selenium-adequate diet. No significant effect was found for the other aldehydes measured. In contrast, the in vivo doses of endogenous ethylene oxide and propylene oxide were lowered in selenium-deficient rats, indicating a 1.7-times faster detoxification rate. This was verified by the lower adduct levels in selenium-deficient rats following intraperitoneal administration of these epoxides at moderate doses. In conclusion, the results seem to reflect the complex changes of induced and reduced enzyme activities in response to selenium deficiency. Measurement of reactive compounds through their adducts to hemoglobin has shown its ability to elucidate the effects of selenium deficiency per se.