A polyglycerol dendrimer (PGD), which is known as a biocompatible compound, was demonstrated as a host molecule for amino acids. PGD of generation 3 (PGD-G3) was found to interact with basic α-amino acids such as l-arginine (Arg) and l-lysine (Lys) in water. The results of isothermal titration calorimetry, 1H NMR, and 1H-1H NOESY NMR measurements revealed that two basic groups in α-amino acids were essential for encapsulation by PGD-G3. An increase in the pKa value of the amino acid side chains (Arg>Lys>His>Glu) increased the binding constant, thus suggesting that the basicity of α-amino acids is an important factor to interact with ether oxygen of PGD-G3. The results demonstrate the utility of PGD-G3 toward incorporation of α-amino acids, peptides, and basic proteins in water.