Zinc alpha2-glycoprotein (ZAG) is present at high concentration in human seminal plasma, and considered as soluble homologue of MHC-I. ZAG is a well-known biomarker for prostate and breast carcinomas. We have purified a naturally occurring complex of ZAG with Prolactin inducible protein (PIP), which is also a well-known biomarker for the same. The ZAG-PIP complex has been isolated and purified by simple chromatographic techniques in a reproducible two-step process, using ion exchange and gel-permeation chromatography and subsequently identified by MS. The complex between ZAG and PIP is formed by non-covalent interactions. The purity and molecular mass was determined by SDS-PAGE, which shows the bands corresponding to 40 kDa and 14 kDa, which were also confirmed by MALDI-TOF. Dynamic light scattering (DLS) experiments also showed hydrodynamic radii corresponding to 54, 40 and 14 kDa for ZAG-PIP complex, ZAG and PIP respectively. The concentration dependent aggregation of this complex has also been observed. Fluorescence analysis reveals that complexes have similar binding affinities as native ZAG, for their proposed ligands like arachidonic acid, polyethylene glycol and synthetic peptide. This is the first report on purification and characterization of a naturally occurring complex of ZAG-PIP in human seminal fluid.