The study describes a mode of non-destructive simultaneous determination of bromine and iodine concentrations, by reactor instrumental neutron activation analysis (INAA) in the regime of short-term activation. Under the conditions of 1-minute activation in the neutron flux of 8.0·1013 n·cm−2·s−1, it was possible to determine reliably as little as 5·10−8 g bromine and about 10−7 g iodine in matrices of a given type and of the mass of about 5 mg dry weight. We applied this method for the determination of Br and I concentrations in the whole rat thyroid gland as well as for the halogen speciation in fractions separated from this organ.