A panel of four hydrophobic adsorbents (butyl-, octyl-, phenyl- and epoxy-Sepharose) was used to examine the selectivity and fractionation of several proteose peptone 3 (PP3) forms from a freeze-dried extract of whey bovine milk. In particular, the effects of altering the ligand type and salt were investigated. The chromatographic studies suggest that PP3 strongly interacts among the three commercial hydrophobic resins leading to a drop off in selectivity, while a complete binding was achieved at low salt concentrations (below 0.5 m) and total elution only with phosphate buffer and/or water stepwise conditions. Only in epoxy–Sepharose was an appreciably selectivity of the several fractions of PP3 present in the initial feedstock attained. Despite the high salt concentration for a complete binding of PP3 (above 1.5 m ammonium sulfate) onto this support, the dual salt system (ammonium sulfate 1 m and sodium citrate 0.8 m) led to a high separation degree of high and low molecular weight forms of PP3. Copyright © 2007 John Wiley & Sons, Ltd.