Abstract The sea surface closely agrees with the marine geoid, a surface of constant gravitational potential. If the observed undulations of the sea surface are adjusted for time-dependent effects, such as tide, currents and wind, the remaining undulations reflect density variations within the Earth. By studying the relative undulations of the mean sea surface instead of the mean sea surface heights relative to the reference ellipsoid, the precision and the resolution of satellite radar altimeter observations can be greatly improved. The noise level can be reduced to a few centimetres and wavelengths as short as a few tens of kilometres can be detected. Satellite radar altimeter data, from the three satellites GEOSAT, SEASAT and GEOS-3 have been combined, to compute a map of the marine geoid in the southern Baltic Sea. Harmonic filtering of the computed sea surface has been applied to separate the long wavelength undulations (220–450 km) of the marine geoid. This wavelength band of the marine geoid in the southern Baltic Sea is characterized by a pronounced gravity low southwest of the Tornquist-Teisseyre (T-T) Zone and a high northeast of this border between the Baltic Shield and central Europe. This gravity low is caused by the lower mass of the crust on the European side of the T-T Zone relative to the crust on the Baltic side of the T-T Zone. Thick accumulations of low-density sediments on the European side, density variations in the crust, or a combination of these, are possible explanations for this negative gravity anomaly. In the eastern part of the Baltic Sea several gravity lows, having similar or higher gravity gradients than those over the T-T Zone, are following a more or less north-southerly trend. The explanation of these very strong mass deficiencies is not clear, but suggests the possibility of an extension of the Central Swedish Gravity Low which continues southward into the Central Baltic Sea Gravity Low. A strong positive gradient in the marine geoid can be observed between the island of Gotland and the Swedish mainland, probably related to the relatively higher density of rocks of the Bergslagen Province.