Stromatolite morphology is usually controlled by a number of biological and environmental factors. In the south-eastern part of the Korean Peninsula, three stromatolite units of the Cretaceous Sinyangdong Formation have been studied with regard to the effect of diagenesis on their morphology. Here, it is proposed that subaerial exposure and meteoric diagenesis are the most significant factors in shaping the stromatolites of the Cretaceous Sinyangdong Formation. Most previous palaeontological and sedimentological studies on stromatolites have concentrated on the environmental and biogenic controls on stromatolite morphology. These include extrinsic factors such as sedimentation rates or current velocities. The main controlling factor on the morphology of the stromatolites in the Sinyangdong Formation is apparently transient subaerial exposure and related meteoric diagenesis. Textural examination of stromatolite samples from three stratigraphic horizons shows a characteristic repetitive pattern of cycles with gradual transition from fibrous calcite to micrite layers, reflecting changes in the hydrological cycle of the lake in which the stromatolites grew. Stromatolite growth was terminated by corroded surfaces indicative of subaerial exposure related to a fall in lake level. The growth pattern of the stromatolites was mostly determined by the morphology of the corroded substrates during subaerial exposure. Furthermore, the internal stromatolite structure was strongly modified by the process of leaching. As a result, growth forms mostly changed from stratiform to columnar mesostructure. This study strongly implies that diagenesis could make a very significant influence on the morphogenesis of lacustrine stromatolites in the geological past.