For optimal nutrient absorption to occur, the enterocyte must express a range of specialist ion-driven carrier proteins that function cooperatively in a linked and mutually dependent fashion. Thus, absorption via the human intestinal H(+)-coupled di/tripeptide transporter (hPepT1) is dependent on maintenance of the trans-apical driving force (the H(+)-electrochemical gradient) established, in part, by brush-border Na(+)/H(+) exchanger (NHE3) activity. This study aimed to examine whether physiologic regulation of NHE3 activity can limit hPepT1 capacity and, therefore, protein absorption after a meal. hPepT1 and NHE3 activities were determined in intact human intestinal epithelial Caco-2 cell monolayers by measurements of [(14)C]glycylsarcosine transport and uptake, (22)Na(+)-influx, H(+)-influx, and H(+)-efflux. Expression of NHE regulatory factors was determined by reverse-transcriptase polymerase chain reaction. Optimal dipeptide transport was observed in the presence of a transapical pH gradient and extracellular Na(+). At apical pH 6.5, and only in Na(+)-containing media, protein kinase A activation (by forskolin or vasoactive intestinal peptide) or selective NHE3 inhibition (by S1611) reduced transepithelial dipeptide transport and cellular accumulation by a reduction in the capacity (without effect on affinity) of dipeptide uptake. Protein kinase A-mediated modulation of intestinal dipeptide absorption is indirect via effects on the apical Na(+)/H(+) exchanger.