Anthropogenic inputs of CO2 are altering ocean chemistry and may alter the role of marine calcifiers in ocean ecosystems. CO2 emissions over the coming centuries may produce changes in ocean pH not seen for millions of years. Laboratory evidence has shown decreased calcification in some species of coccolithophores, foraminifera, corals and pteropods in response to CO2 enrichment. However, in situ observations of calcification in marine organisms are limited, especially for the aragonitic pteropods. This group of pelagic molluscs are likely to be more sensitive to changes in carbonate chemistry than calcite producers such as foraminifera and coccolithophores. Here we present observations of pteropod shell-weight and flux from 1997–2006 in sediment traps deployed at 47° S, 142° E at 2000 meters below sea surface in the Southern Ocean. A decadal trend of –1.17±0.47 μg yr 1 (P=0.02) in mean shell weight in the pteropod Limacina helicina antarctica forma antarctica suggests a small but detectable reduction in calcification. Gaps in the data make it difficult to state with certainty the significance of the trend. However, this data set represents the first attempt to estimate interannual variations in pteropod calcification and establish a benchmark against which future impacts of ocean acidification may be detected. Contributions of Limacina helicina antarctica morphotypes to the total pteropod flux were also reduced over the decade. We suggest these small though discernible trends are due to changing carbonate chemistry in the Subantarctic, as other oceanographic variables show no clear decadal trends. With CO2 continuing to enter the ocean such impacts on pteropods and other marine calcifiers could result in changes to the distribution of species and the structure of Southern Ocean ecosystems.