Avian eggshell fragments recovered from both paleontological and archaeological deposits contain a cache of well-preserved ancient DNA. Here, we describe an extraction protocol that has been optimized to maximize the recovery of ancient DNA from fossil eggshell and minimize the co-purification of PCR inhibitors. In this method, fossil eggshell fragments are powdered, then digested and heated to release DNA from the calcite matrix. The digest then undergoes a concentration step before purification and washing using silica columns. The method has been used to recover aDNA from the eggshell of many avian species including moa, elephant birds, and emu, up to 19,000 years old.