The surface sediment of the Chilean Inlets Region has been extensively studied during three major cruises: Cimar Fiordo Cruise 1 in the Upper Area (41°20′S to 46°40′S), Cimar Fiordo Cruise 2 in the Middle Area (46°40′to 47°10′S) and Cimar Fiordo Cruise 3 in the Lower Area (52°19′S to 55°58′S). Total and organic carbon were analysed in 174 sediment samples with an LECO CR-12 elemental analyser. Organic nitrogen was determined using the micro-Kjeldhal technique. Methods were calibrated against standard reference materials certified by the National Institute of Standards and Technology, U.S.A.The study areas were geographically segregated into nine zones according to carbon and nitrogen concentration and distribution. Three of the areas, with comparatively high organic carbon (>1·6%) and organic nitrogen (>0·2%) abundance, were associated with geographically protected inlets and productive planktonic zones. A further four areas with comparatively low organic carbon (In the Upper Area the zonal definition followed a north–south pattern due to the presence of the Corcovado Gulf, which is under the oceanic influence of the West Wind Drift current. Conversely, the Middle Area followed an east–west pattern arising from the ‘Campo de Hielo Norte’ and ‘Campo de Hielo Sur’ glacial fields. A southward trend of diminishing organic carbon content was also noted throughout the Inlets Region.Based on the computed carbon-nitrogen ratios for the previous zones, (C:N range of 5·4 to 11·4), the origin of the organic matter present in the surface sediment was deduced. The C:N values can be chiefly associated to sediment of marine origin, with some degree of remineralization. The edaphic input did not appear to play an important role. Furthermore, the results suggest that the anthropogenic influence on the region is minimal, and thus could be considered as a pristine environment.