An endonuclease from human placenta has been purified to apparent homogeneity, which acts specifically on DNA containing either apurinic or apyrimidinic sites. The isolation procedure, which results in a 20,000-fold purification and an overall yield of 15%, employs chromatography on a gel of octyl succinic anhydride coupled to agarose by diaminohexane spacers, isoelectric focusing, Sephadex G-75 chromatography, and DNA agarose affinity chromatography. Under conditions in which proteolysis is minimized, this enzyme appears to be the major species of apurinic/apyrimidinic endonuclease. The endonuclease is a monomeric protein with an apparent Mr = 37,000 as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The enzyme has a pI of 7.4-7.6, requires Mg2+, is partially stimulated by Mn2+, and is inhibited by EDTA. It has no detectable exonuclease or phosphomonoesterase activity.