The Belize barrier and atoll reefs represent one of the largest reef structures in the Atlantic Ocean. The southern shelf of Belize is a classic location of a modern mixed carbonate–siliciclastic system. Whereas knowledge of the Holocene deposits in the area is extensive, data on the Pleistocene system are fragmentary. Open questions include: (i) the nature of the reef foundations (carbonate versus siliciclastics); (ii) the ages of the deposits including the initiation of the barrier reef; and (iii) the response of the mixed system to sealevel fluctuations. The results of a study of borings on the southern Belize shelf are presented here. Six, up to 105 m long borings were made to better understand the history of this important mixed system. Uranium-series dating in the Pleistocene was not possible because of diagenetic alteration; however, lithostratigraphy, strontium isotopes and calcareous nannofossil biostratigraphy were used to constrain stratigraphic ages. Results support the contention that the Quaternary development in Belize was quite similar to that of other major barrier reefs such as the Florida Reef Tract and, further afield, the Great Barrier and the New Caledonian Barrier Reefs. All of these barrier reefs are mixed carbonate–siliciclastic systems and significant reef growth only began after the onset of high-amplitude, eccentricity-controlled sea-level changes and as late as during the exceptionally long and warm marine isotope stage 11, some 400 ka. In Belize, Early Pleistocene sections at bases of borings include mollusc-rich wackestones, rare coral packstones and marls, which were deposited under low to moderate energy conditions in a ramp setting before ca 900 ka, during the high sea-levels of marine isotope stage 25 and possibly earlier (marine isotope stage 31 or 37). The Belize shelf was subaerially exposed for most of the mid-Pleistocene and was dominated by siliciclastic sedimentation, possibly during marine isotope stages 24 to 12 when highstands were comparatively low. Continuous reefs at the shelf margin were developing during highstands. In the Late Pleistocene, beginning with the long and high highstand of marine isotope stage 11 (some 400 ka), the southern shelf was flooded entirely and carbonates started to dominate once more. Reefs developed on top of siliciclastic deposits on the shelf. A continuous barrier reef came into existence and largely developed on top of carbonates at the shelf margin. During Late Pleistocene lowstands, siliciclastics presumably no longer reached the shelf margin because of the topographic high of the barrier reef platform. The Quaternary Belize example may serve as a model for reconstructing ancient mixed systems in icehouse worlds, however, any extrapolations are limited by the fact that fast-growing Scleractinian reef-builders had not yet evolved in the Palaeozoic.