The function of the secretory pathway is dependent on multiple protein-protein interactions at various stages. Currently, such interactions are mainly studied using physical methods that document direct contact or affinity in vitro. The development of vital fluorescence imaging as well as quantitative protein transport assays opens up the implementation of in vivo approaches which can be used to verify models based on in vitro work. The purpose of this review is to provide an overview of the various approaches involving living cells to resolve interactions between proteins that control complex mechanisms. In particular, it is illustrated how combinations of several methods can establish whether postulated interactions are of biological relevance or due to artefacts inherent to the experimental set-up.