Phosphodiesterase I from the venom of Bothrops atrox has been purified by successive chromatography on phosphocellulose P-11, hydroxyapatite, and DEAE-cellulose DE 52. The final product gave a single band on sodium dodecylsulfate-polyacrylamide gels and was free of endonuclease, 5' -nucleotidase, and unspecific alkaline phosphatase activity. It was concentrated in an Amicon ultrafiltrator without loss of activity and could be stored in 10 mM magnesium acetate and 10% glycerol at 4 degrees C for at least a year. Under optimal conditions, the enzyme reaction required 15 mM Mg2+ and a pH of 9.2. Phosphodiesterase I is relatively thermostable and, in the presence of a macromolecular substrate, was not denatured after 4 h at 55 degrees C. The pure enzyme offers new possibilities for sequence studies on highly structured nucleic acids at elevated temperatures.