This case report correlates impaired cyclosporine absorption from the traditional oral formulation in a 9-year-old liver transplant recipient with subsequent acute allograft rejection. Although impaired absorption in this patient was documented by cyclosporine pharmacokinetic profiling (steady-state area under the cyclosporine concentration-time curve or AUC), no indication was evident from the pre-dose cyclosporine trough level, which was within the typical target range of blood concentrations. However, when the subject received the microemulsion formulation of cyclosporine the AUC value reflected an adequate absorption pattern. We recommend that if malabsorption is suspected in the de novo pediatric liver transplant patient, then single-sample pre-dose trough cyclosporine levels should not be relied on as an indicator of sufficient immunosuppression and that a limited sampling strategy be used to confirm or rule out impaired absorption.