Denitrification in lakes significantly reduces the nitrogen (N) load from land to oceans, but the factors controlling it remain poorly understood. Therefore, interlake variation of denitrification in sediments of small to medium-sized lakes (from 0.03 to 17.8 km2) was studied across different geographical scales. At the local scale, the denitrification rates and sediment microbial communities were studied in 4 boreal lakes in close proximity (within 20 km) using the isotope pairing technique (IPT) and molecular methods. These local scale data were combined with previously published data on denitrification rates from 10 other European lakes to extend the analysis to the regional (boreal area) and continental (boreal and temperate areas) scales. Denitrification varied considerably among lakes, ranging from ~50 to ~600, ~0 to ~600 and ~0 to ~12900 μmol N m-2 d-1 at the local, regional and continental scales, respectively. This variation was primarily due to nitrate availability. The structure of the denitrifier community studied at the local scale was independent of the denitrification rates but varied among lakes correlating with nitrate availability and sediment organic content. Removal of nitrate and total N load by denitrification was less efficient in boreal than in temperate lakes. In addition, a meta-analysis of published N mass balance data indicates that the total N retention (denitrification + N sedimentation) is less efficient in boreal than in temperate lakes. Anaerobic ammonium oxidation (anammox) was studied at the local scale but was not detected, although (based on molecular markers) several anammox genera were present in the sediments.