The total stratospheric organic chlorine and bromine burden was derived from balloon-borne measurements in the tropics (Teresina, Brazil, 5°04´ S, 42°52´ W) in 2005. Whole air samples were collected cryogenically at altitudes between 15 and 34 km. For the first time, we report measurements of a set of 28 chlorinated and brominated substances in the tropical upper troposphere and stratosphere including ten substances with an atmospheric lifetime of less than half a year. The substances were quantified using pre-concentration techniques followed by Gas Chromatography with Mass Spectrometric detection. In the tropical tropopause layer at altitudes between 15 and 17 km we found 1.1–1.4% of the chlorine and 6–8% of the bromine to be present in the form of very short-lived organic compounds. By combining the data with tropospheric reference data and age of air observations the abundances of inorganic chlorine and bromine (Cly and Bry) were derived. At an altitude of 34 km we calculated 3062 ppt of Cly and 17.5 ppt of Bry from the decomposition of both long- and short-lived organic source gases. Furthermore we present indications for the presence of additional organic brominated substances in the tropical upper troposphere and stratosphere.