The objective of this investigation was to quantitate the effect of binding on the iontophoretic transport of a series of amino acids. The diffusivity and concentration in the stratum corneum and viable skin were estimated from the passive permeation profiles through whole and stripped skin. Using these parameters and the Langmuir binding parameters from equilibrium binding studies, the passive permeation and desorption profiles were simulated using a bilayer skin permeation model. The parameters were adjusted until convergence with experimental data was achieved. Then the iontophoretic profiles were simulated, using the parameters from the simulated passive permeation studies, an estimate of convective flow from the flux of tritiated water, and measurement of the potential across the skin. The overall effect of binding on the iontophoretic profiles was found to dampen the effect of the iontophoresis treatment; the profiles appear flatter, and the transition to passive diffusion less distinct compared to profiles which do not include the binding parameters. It also appears that the degree of skin hydration has a substantial effect on the shape of the iontophoretic profile, such that approximately 50% of the enhancement in the iontophoretic profile of freshly excised skin continues after treatment.