Improved methods are provided for purifying selected carcinoembryonic antigen (CEA) family member proteins. Disclosed method steps include cation-exchange chromatography below pH 4.0 and size-exclusion chromatography, and do not include use of perchloric acid or antibody affinity steps. The resulting purified proteins are of at least 90% purity, substantially free of cross-reacting antigens, substantially free of CA19-9, substantially free of endotoxins, and substantially free of antibodies. Purities of greater than 98% have been achieved. Purified CEA family member proteins used as reference standards, in pharmaceutical carriers, and formulated as vaccines are disclosed. The purification, compositions, and use of CEA family member proteins containing altered immunogenic epitopes are also disclosed.