Transpose-AMIP II is an international model comparison project in which climate models are run in weather forecast mode. The project is running alongside CMIP5 and allows processes operating in climate models to be evaluated, and the origin of climatological biases explored, by examining the evolution of the model from a state in which the large-scale dynamics, temperature and humidity structures are constrained through use of common analyses. This study presents the Transpose-AMIP II experimental design, and provides and example of how such hindcasts can be used. The development of cloud biases over the Southern Ocean is examined in several models. This region is known to be problematic for many models. Several models share a climatological bias of too little reflected shortwave radiation in the region. This is found to occur mainly behind cold fronts and be associated with relatively stable lower-tropospheric conditions. Investigation of a typical case reveals the models to simulate cloud that is too optically and geometrically thin with an inversion which is too low. The evolution of the models within the first few hours suggests these conditions are particularly sensitive and a positive feedback can develop that thins the cloud layer and alters boundary layer structure. In at least one model, the lack of sufficient vertical resolution to properly represent the boundary layer structure appears to be a factor.