The objective of this research was to develop a rapid, sensitive and reliable method for the separation of phosphonodipeptide prodrugs and parent compounds to facilitate the evaluation of cell permeation using in vitro cell culture models. Separation was accomplished isocratically within 10.0 min using a C18 (150x4.6 mm I.D., 3 microm) reversed-phase column. The mobile phase consisted of 5 mM tetrahexyl ammonium (ion-pair reagent) in 0.02 M phosphate buffer pH 6.5-acetonitrile (48.5:51.5, v/v). The flow-rate was 1.1 ml/min with detection at 221 nm. The standard curves were linear (r2>0.999) over the concentration range 1-100 microM. The method was reliable and reproducible, with the limit of quantitation being 1 microM (25 ng on column).