The 2-keto-3-deoxygluconate aldolases (KDGAs) isolated from Sulfolobus species convert pyruvate and glyceraldehyde reversibly into 2-keto-3-deoxygluconate and -galactonate. As a result of their high thermostability and activity on nonphosphorylated substrates, KDGA enzymes have potential as biocatalysts for the production of building blocks for fine chemical and pharmaceutical applications. Up to now, wild-type enzymes have only shown moderate stereocontrol for their natural reaction. However, if a set of azido-functionalized aldehydes were applied as alternative acceptors in the reaction with pyruvate, the stereoselectivity was strongly increased to give enantiomeric or diastereomeric excess values up to 97 %. The Sulfolobus acidocaldarius KDGA displayed a higher stereoselectivity than Sulfolobus solfataricus KDGA for all tested reactions. The azido-containing products are useful chiral intermediates in the synthesis of nitrogen heterocycles.