We present a general stratigraphic synthesis for the Upper Rhine Graben (URG) and the Swiss Molasse Basin (SMB) from Eocene to Pliocene times. The stratigraphic data were compiled both from literature and from research carried out by the authors during the past 6 years ; an index of the stratigraphically most important localitites is provided. We distinguish 14 geographical areas from the Helvetic domain in the South to the Hanau Basin in the North. For each geographical area, we give a synthesis of the biostratigraphy, lithofacies, and chronostratigraphic ranges. The relationships between this stratigraphic record and the global sea-level changes are generally disturbed by the geodynamic (e.g., subsidence) evolution of the basins. However, global sea-level changes probably affected the dynamic of transgression–regression in the URG (e.g., Middle Pechelbronn Beds and Serie Grise corresponding with sea-level rise between Ru1/Ru2 and Ru2/Ru3 sequences, respectively) as well as in the Molasse basin (regression of the UMM corresponding with the sea-level drop at the Ch1 sequence). The URGENT-project (Upper Rhine Graben evolution and neotectonics) provided an unique opportunity to carry out and present this synthesis. Discussions with scientists addressing sedimentology, tectonics, geophysics and geochemistry permitted the comparison of the sedimentary history and stratigraphy of the basin with processes controlling its geodynamic evolution. Data presented here back up the palaeogeographic reconstructions presented in a companion paper by the same authors (see Berger et al. in Int J Earth Sci 2005).