A new method for enrichment of phosphopeptides in complex mixtures derived by proteolytic digestion of biological samples has been developed. The method is based on calcium phosphate precipitation of the phosphopeptides prior to further enrichment with established affinity enrichment methods. Calcium phosphate precipitation combined with phosphopeptide enrichment using immobilized metal ion affinity chromatography (Fe(III)-IMAC) provided highly selective enrichment of phosphopeptides. Application of the method to a complex peptides sample derived from rice embryo resulted in more than 90% phosphopeptides in the enriched sample as determined by mass spectrometry. Introduction of a two step IMAC enrichment procedure after calcium phosphate precipitation resulted in observation of an increased number of phosphopeptides by separating the singly and multiply phosphorylated peptides in different fractions.