The enantioselectivity of two protein chiral stationary phases, alpha1 acid glycoprotein (AGP) and ovomucoid protein (OVM) are compared. Neutral, basic and acidic pharmaceutical compounds were screened on both stationary phases. Selected parameters such as mobile phase pH, temperature, and organic modifier were varied in order to achieve chiral separations. Relations between the enantioselectivities of the two stationary phases and the properties of the compounds (acidity, basicity, structure of molecule) were also investigated. The OVM column tends to separate larger molecules better than the AGP column. Reversal of elution order for some compounds was observed on the two columns under similar experimental conditions, or with the same column as a function of pH and organic modifier. Many practical aspects were also discussed.