Protein denaturation, common in hydrophobic adsorption systems, causes misinterpretation of adsorption mechanisms, interferes with analysis in analytical chromatography, and complicates the design of large-scale adsorption processes. A detailed adsorption model isolates the effects due to denaturation from those due to mass transfer and intrinsic adsorption kinetics. The model is verified using protein gradient elution data. Simulations establish that typical symptoms of denaturation in frontal and elution chromatograms include sensitivity to changes in feed composition, column length, particle size, and operating conditions (feed size, flow rate, and column history). When a denatured species adsorbs irreversibly, the elution chromatogram shows decreasing peak area with increasing incubation time and apparent adsorption hysteresis over repeated cycles. In gradient elution, the peak elution order, resolution, and relative peak height depend highly on modulator properties and operating conditions. Interfering species limit solid-phase induced denaturation by competing for binding sites. Strategies for detecting and minimizing denaturation are proposed.