The present invention provides a method for the purification of complexes comprising a stress protein complexed to a peptide or peptide fragment, from a source mixture, typically a cell lysate. The improved method of the invention provides for protein complexes to be purified using ion exchange based methods, without the need to use chemicals such as chaotropes and ampholytes. The purified complexes can be used as the immunogenic determinant in vaccine compositions for the treatment or prevention of infectious diseases or cancerous conditions.