The present invention provides formulations that prevent loss and damage of PEG-interferon alpha conjugates during and following lyophilization. The formulations of the present invention protect PEG-interferon alpha conjugates from loss and degradation during the lyophilization process, as well as degradation during subsequent storage. The formulations of the present invention are suitable for protection of PEG-interferon alpha conjugates from various types of degradation, including, but not limited to loss of biological activity and changes in the degree and/or nature of conjugation. A preferred PEG-interferon alpha conjugate protectable in the formulations of the present invention is an interferon alpha-2b-polyethylene glycol (12,000) conjugate.