The Eastern Mediterranean hosts a variety of active cold seep systems, such as gas chimneys, mud volcanoes and pockmarks, in water depths of 500 to 3200 m. As part of the NAUTINIL expedition in 2003, the sediments of cold seeps on the Nile Deep Sea Fan (NDSF) were sampled for the first time for biogeochemical and microbiological analyses. Here we compare rates of the anaerobic oxidation of methane (AOM) and sulfate reduction (SR) as well as the microbial community structure of a variety of cold seep systems including mud volcanoes, pockmarks and brine seeps. Our results revealed strong differences in microbial activity among the different seep systems of the Eastern, Central and Western provinces of the NDSF, as well as the Olimpi field (Central Mediterranean Ridge). Integrated over a sediment depth of 10 cm below the seafloor, SR rates ranged from 0.1-66 mmol m- 2 d- 1 and AOM rates from 0.1-3.6 mmol m- 2 d- 1. SR was often considerably higher than methane oxidation, indicating that electron donors other than methane were utilized. In general, the lowest rates were associated with pockmarks and carbonate pavements, and highest rates with bacterial mats above the gassy sediments of mud volcano centers. 16S rRNA gene analysis and fluorescence in situ hybridization (FISH), revealed the presence of all known groups of marine methane oxidizing Archaea (i.e. ANME-1, -2, -3) and also of methane oxidizing Bacteria (i.e. Methylobacter sp. and relatives) in some seep sediments. Presumably syntrophic sulfate-reducing bacterial partners of ANMEs were also detected in association with the ANMEs. Several ANMEs formed consortia with unknown bacterial partners. The microbial community structure reflected the presence of typical seep microorganisms at all sites investigated, but differed to varying extents between the different types of seeps. Despite the high availability of methane and sulfate, methanotrophic microbial activity and biomass were lower at the seeps of the Eastern Mediterranean compared to those of other continental margins for unknown reasons. © 2009 Elsevier B.V. All rights reserved.