Proteins having an epidermal growth factor-like binding region, such as thrombomodulin, may be recovered and purified on a anion exchange resin, such as a polyethyleneimine resin. Conditioned medium containing recombinantly produced protein is applied to the resin under conditions of pH and ionic strength selected to result in specific binding of the protein to the resin. The column is then washed to remove non-bound proteins and bound proteins other than the desired protein to be separated. The desired protein is then eluted from the column and collected in a medium. Further purification, concentration, and other treatment of the protein may be performed by conventional techniques.