This paper has described about preparation of $Zr^{4+}$ affinity column based on the poly(styrene-co- gly-cidyl methacrylate) prepared by emulsion polymerization of styrene and glycidyl methacrylate in order to isolate phosphopeptide. The $Zr^{4+}$ ions were introduced after the phophonation of an epoxy group on polymeric microspheres. The successful preparation of $Zr^{4+}$-immobilized polymeric microsphere stationary phase was confirmed through Fourier transform infrared spectra, optical microscopy, scanning electron microscopy, X-ray photoelectron spectra and inductively coupled plasma-atomic emission spectrometer. The separation efficiency for $Zr^{4+}$ affinity column prepared by slurry packing was tested to phosphonated casein and dephosphonated casein. The resolution time (min) of the phosphonated casein was higher than that of dephosphated casein for $Zr^{4+}$ affinity polymeric microsphere by liquid chromatography. This $Zr^{4+}$ affinity column can be used for isolation of phosphonated casein from casein using liquid chromatography.