The distributions of carotenoid pigments were studied in recent and postglacial sediments collected in the Gotland Basin, in the northern part of the Baltic proper, and in the eastern Gulf of Finland in May 1999. The aim was to provide a systematic, historical review of the occurrence and intensity of cyanobacterial blooms in the Baltic Sea in recent centuries. The presence of pigments was determined using high-pressure liquid chromatography (HPLC), with attention mainly focused on pigments considered as markers for cyanobacteria. The pigment concentrations in sediments from the 3 sampling locations were found to differ markedly. In general, concentrations were highest in sediments from the Gotland Basin, and lowest in sediments from the eastern Gulf of Finland. In all 3 cores echinenone was the dominant carotenoid in the topmost layer of the sediment (0–1 cm). In the deeper sections of the cores, myxoxanthophyll and zeaxanthin dominated. To our knowledge, this is first time that myxoxanthophyll and echinenone have been detected in Baltic Sea sediments from the early Litorina stage. The decrease in the pigment content with sediment depth coincides with a decrease in carbon content, and also fits in with general historical records of the occurrence and intensity of cyanobacterial blooms in the Baltic Sea, which show that cyanobacterial blooms were seldom recorded before World War II.