We performed a comprehensive analysis of ghrelin release-modulating activity of a dipeptide library using MGN3-1, a ghrelin-producing cell line. We found that most dipeptides suppress ghrelin secretion, whereas the N-terminal Ser-containing dipeptides and a few others stimulate it. N-terminal amino acid residues, but not C-terminal residues, play a dominant role in the effects of dipeptides. Among dipeptides, Leu-Ile (LI) and Ser-Val (SV) most strongly suppress and stimulate ghrelin secretion, respectively. LI activates Gi signaling and SV acts via the MAPK pathway. Orally administered LI and SV reduce and increase plasma ghrelin levels and food intake in mice, respectively. In conclusion, LI and SV, found based on the comprehensive screening of a dipeptide library, modulate ghrelin secretion in vitro and in vivo.