Affinity chromatography is an effective method for the purification of biological material. A mathematical model has been set up by the material balance in the chromatographic column and the approximate solution has been obtained by the Gaussian expansion equation which expands in the derivatives of normal probability density function. The coefficients of the derivatives are functions of moments which are obtained from the Laplace transformation of the differential equations. Affinity chromatography is affected by changing of pH. Ionization model has been developed to explain the phenomena of pH effect on the affinity chromatography. The relation between the mathematical model and the ionization model is shown.