Abstract: The present invention provides, among other things, methods of purifying or recovering proteins, in particular, small modular immunopharmaceutical (SMIPs™) proteins, from protein preparations containing high molecular weight (HMW) aggregates and other impurities based on hydroxyapatite chromatography. In some embodiments, the hydroxyapatite chromatography is used in combination with affinity chromatography and/or ion exchange chromatography. In some embodiments, inventive methods according to the invention involve no more than three chromatography steps. The present invention also provides proteins such as SMIPs™ purified according to the invention and pharmaceutical compositions containing the same.