The present invention relates to methods for purifying immunogenic, prophylactically and therapeutically effective complexes of modified heat shock proteins noncovalently associated with antigenic peptides of cancer or infected cells. The claimed methods comprise the constructing of a nucleotide sequence encoding a secretable modified heat shock protein, expressing the sequence in an appropriate host cell, recovering the immunogenic complexes from the cell culture and the cells, and purifying the immunogenic complexes by affinity chromatography. Large amounts of such immunogenic complexes can be obtained by large-scale culturing of host cells containing the genetic sequence. The complexes can be used as a vaccine to elicit specific immune responses against cancer or infected cells, and to treat or prevent cancer or infectious diseases.