The vegetation–atmosphere-exchange is an important process controlling the atmospheric concentration of various volatile organic compounds (VOCs) that play a major role in atmospheric chemistry. However, the quantification of VOC exchange on the ecosystem scale is still an analytical challenge. In the present study we tested and applied a proton-transfer-reaction mass spectrometry system (PTR-MS) for the measurement of biogenic VOCs in a mixed deciduous forest. VOC concentrations were calculated from the raw instrument signals based on physical principles. This method allows a consistent quantification also of compounds for which regular calibration with a gas standard is not available. It requires a regular and careful investigation of the mass-dependent ion detection characteristics of the PTR-MS, which otherwise could become a considerable error source. The PTR-MS method was tested in the laboratory for a range of oxygenated and non-oxygenated VOCs using a permeation source. The agreement was within 16% or better, which is well within the expected uncertainty. During the field measurement campaign in a deciduous forest stand, an on-line intercomparison with a state-of-the-art gas-chromatography system showed a generally good agreement. However, the relatively low ambient VOC concentrations revealed some systematic difference for acetone and isoprene, that may indicate an error in the determination of the PTR-MS offset or an interference of an unidentified isobaric compound on the detected ion mass. With the presentation of selected field results, we demonstrate the ability of the PTR-MS system to measure continuous vertical concentration profiles of biogenic VOCs throughout a forest canopy at a time resolution of 20 min. The resulting datasets provide valuable information for the study of the interactions between emission, photochemical transformation and transport processes within and above the forest canopy.