Amino acid-derived gemini surfactants arise as a potentially good alternative to the more conventional lipid and synthetic catanionic systems in view of their enhanced interfacial properties, increased chemical stability, and low toxicity. The presence of an amino acid as the polar headgroup allows toxicity reduction, with the simultaneous increase of biodegradability. For these compounds, the establishment of structure/function relationships from the assessment of their basic aggregation properties is therefore of the utmost interest, e.g., in the design of operative self-assembled systems (e.g., liposomes, nanotubes, etc). In this context, the study of the thermal phase behavior of the dry surfactants is a natural, straightforward first step, the more so as thermotropic liquid crystals are also relevant for practical applications. In this work, several lysine-based amphiphiles with a gemini-like configuration have been synthesized, with the amino acid side chain as the spacer group. The molecules are either esters (neutral, with C6-C12 even chains) or sodium carboxylates (anionic, with C6-C12 even chains). Upon increasing the temperature, different crystalline (cr) and liquid-crystalline (1c) phases have been detected and the corresponding thermodynamic and structural parameters determined by a combination of differential scanning calorimetry, polarizing light microscopy and small-angle X-ray scattering. The phase behavior of the amphiphiles is highly dependent on both the chain length and the presence of charge on the headgroup, with significant differences occurring within and between each group of molecules. The C6 and C8 esters form reverse hexagonal cr and lc phases, while C10 and C12 self-assemble into smectic cr and lc structures, with C10 showing also a reverse hexagonal lc phase prior to isotropization. All the carboxylate derivatives form smectic lc phases at high enough temperature prior to isotropization. The rationalization of the phase behavior and phase transition energetics of the compounds has been put forth on the basis of the intermolecular interactions at stake (van der Waals, H-bonding, electrostatic, and packing) and the molecular shape of the amphiphile.