Abstract. We present novel measurements of five short-lived brominated source gases (CH2Br2, CHBr3, CH2ClBr, CHCl2Br and CHClBr2). These rather short-lived gases are an important source of bromine to the stratosphere, where they can lead to depletion of ozone. The measurements have been obtained using an in situ gas chromatography and mass spectrometry (GC–MS) system on board the High Altitude and Long Range Research Aircraft (HALO). The instrument is extremely sensitive due to the use of chemical ionization, allowing detection limits in the lower parts per quadrillion (ppq, 10−15) range. Data from three campaigns using HALO are presented, where the upper troposphere and lower stratosphere (UTLS) of the northern hemispheric mid-to-high latitudes were sampled during winter and during late summer to early fall. We show that an observed decrease with altitude in the stratosphere is consistent with the relative lifetimes of the different compounds. Distributions of the five source gases and total organic bromine just below the tropopause show an increase in mixing ratio with latitude, in particular during polar winter. This increase in mixing ratio is explained by increasing lifetimes at higher latitudes during winter. As the mixing ratios at the extratropical tropopause are generally higher than those derived for the tropical tropopause, extratropical troposphere-to-stratosphere transport will result in elevated levels of organic bromine in comparison to air transported over the tropical tropopause. The observations are compared to model estimates using different emission scenarios. A scenario with emissions mainly confined to low latitudes cannot reproduce the observed latitudinal distributions and will tend to overestimate organic bromine input through the tropical tropopause from CH2Br2 and CHBr3. Consequently, the scenario also overestimates the amount of brominated organic gases in the stratosphere. The two scenarios with the highest overall emissions of CH2Br2 tend to overestimate mixing ratios at the tropical tropopause, but they are in much better agreement with extratropical tropopause mixing ratios. This shows that not only total emissions but also latitudinal distributions in the emissions are of importance. While an increase in tropopause mixing ratios with latitude is reproduced with all emission scenarios during winter, the simulated extratropical tropopause mixing ratios are on average lower than the observations during late summer to fall. We show that a good knowledge of the latitudinal distribution of tropopause mixing ratios and of the fractional contributions of tropical and extratropical air is needed to derive stratospheric inorganic bromine in the lowermost stratosphere from observations. In a sensitivity study we find maximum differences of a factor 2 in inorganic bromine in the lowermost stratosphere from source gas injection derived from observations and model outputs. The discrepancies depend on the emission scenarios and the assumed contributions from different source regions. Using better emission scenarios and reasonable assumptions on fractional contribution from the different source regions, the differences in inorganic bromine from source gas injection between model and observations is usually on the order of 1 ppt or less. We conclude that a good representation of the contributions of different source regions is required in models for a robust assessment of the role of short-lived halogen source gases on ozone depletion in the UTLS.