Long sediment cores were collected in spring 2006 from Lake Petén Itzá, northern Guatemala, in water depths ranging from 30 to 150 m, as part of an International Continental Scientific Drilling Program project. The sediment records from deep water consist mainly of alternating clay, gypsum and carbonate units and, in at least two drill sites, extend back >200 kyr. Most of the lithostratigraphic units are traceable throughout the basin along seismic reflections that serve as seismic stratigraphic boundaries and suggest that the lithostratigraphy can be used to infer regional palaeoenvironmental changes. A revised seismic stratigraphy was established on the basis of integrated lithological and seismic reflection data from the basin. From ca 200 to ca 85 ka, sediments are dominated by carbonate-clay silt, often interbedded with sandy turbidites, indicating a sediment regime dominated by detrital sedimentation in a relatively humid climate. At ca 85 ka, an exposure horizon consisting of gravels, coarse sand and terrestrial gastropods marks a lake lowstand or partial basin desiccation, indicating dry climate conditions. From ca 85 to ca 48 ka, transgressive carbonate-clay sediments, overlain by deep-water clays, suggest a lake level rise and subsequent stabilization at high stage. From ca 48 ka to present, the lithology is characterized by alternating clay and gypsum units. Gypsum deposition correlates with Heinrich Events (i.e. dry climate), whereas clay units coincide with more humid interstadials.