Denitrification is a main branch of the global nitrogen cycle. In the past ten years unravelling the underlying biochemistry and genetics has proceeded at an increasing pace. Fungal denitrification has become a new field. The biochemical investigation of denitrification has culminated in the description of the crystal structures of the two types of nitrite reductases. The N2O reductase shares with cytochrome c oxidase the CuA center as a structurally novel metal site. The cytochrome b subunit of NO reductase has a striking conservation of heme-binding transmembrane segments versus the subunit I of cytochrome c oxidase. Another putative denitrification gene product shows structural relation to the subunit III of the oxidase. N2O reductase and NO reductase may be ancestors of energy-conserving enzymes of the heme-copper oxidase superfamily. More than 30 genes for denitrification are located in a >30-kb cluster in Pseudomonas stutzeri, and comparable gene clusters have been identified in Pseudomonas aeruginosa and Paracoccus denitrificans. Genes necessary for nitrite reduction and NO reduction have a mosaic arrangement with very few conserved locations within these clusters and relative to each other.