Data for ciliate abundance, biomass and taxonomic composition, along with relevant biotic and abiotic parameters, were gathered from 9 profiles in the Bellingshausen and Amundsen Seas (Southern Ocean) during late summer and early autumn 2006. A total of 70 species were found, with extrapolations using species accumulation curves suggesting that the true diversity lay between 77 and 90 species. Ciliate abundance and biomass were low, but not unexpectedly so, given the time of year and productivity of the system. Despite the harsh environment, species richness was not less than that found for protists from more temperate habitats, and declined with depth less steeply than abundance and biomass. Ciliate biomass was driven primarily by productivity, with tighter correlations between chlorophyll a (chl a) and either abundance or biomass than those seen from other marine systems. Community composition was also driven by productivity, with a principal components analysis (PCA) on species data showing the first axis strongly correlated with productivity parameters. Moreover, species abundance distributions (SADs) were most often best matched by the geometric distribution, thought to be expected when relatively few parameters determine species distributions. Abundance and diversity were also compared using settled and quantitative protargol stain (QPS) samples. QPS samples had lower mean abundance, higher total species richness and higher taxonomic resolution than did the settled samples. However, per-sample species (or morphotype) richness was the same in settled and QPS samples.