The self‐assembly in aqueous solution of three Fmoc‐amino acids with hydrophobic (aliphatic or aromatic, alanine or phenylalanine) or hydrophilic cationic residues (arginine) is compared. The critical aggregation concentrations were obtained using intrinsic fluorescence or fluorescence probe measurements, and conformation was probed using circular dichroism spectroscopy. Self‐assembled nanostructures were imaged using cryo‐transmission electron microscopy and small‐angle X‐ray scattering (SAXS). Fmoc‐Ala is found to form remarkable structures comprising extended fibril‐like objects nucleating from spherical cores. In contrast, Fmoc‐Arg self‐assembles into plate‐like crystals. Fmoc‐Phe forms extended structures, in a mixture of straight and twisted fibrils coexisting with nanotapes. Spontaneous flow alignment of solutions of Fmoc‐Phe assemblies is observed by SAXS. The cytocompatibility of the three Fmoc‐amino acids was also compared via MTT [3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide] mitochondrial activity assays. All three Fmoc‐amino acids are cytocompatible with L929 fibroblasts at low concentration, and Fmoc‐Arg shows cell viability up to comparatively high concentration (0.63 mM).