The self-assembly and characterization of water-soluble calix[4]arene-based molecular capsules (12) is reported. The assemblies are the result of ionic interactions between negatively charged calix[4]arenes 1 a and 1 b, functionalized at the upper rim with amino acid moieties, and a positively charged tetraamidiniumcalix[4]arene 2. The formation of the molecular capsules is studied by (1)H NMR spectroscopy, ESI mass spectrometry (ESI-MS), and isothermal titration calorimetry (ITC). A molecular docking protocol was used to identify potential guest molecules for the self-assembled capsule 1 a2. Experimental guest encapsulation studies indicate that capsule 1 a2 is an effective host for both charged (N-methylquinuclidinium cation) and neutral molecules (6-amino-2-methylquinoline) in water.