We report on a high-resolution X-ray photoemission spectroscopy study on molecular-thick layers of L-cysteine deposited under ultrahigh vacuum conditions on Au(110). The analysis of core level shifts allowed us to distinguish unambiguously the states of the first-layer molecules from those of molecules belonging to the second layer. The first-layer molecules strongly interact with the metal through their sulfur headgroup. The multipeaked structure of the N 1s, O 1s, and C 1s core levels is interpreted in terms of different molecular moieties. The neutral acidic fraction (HSCH2CH(NH2)COOH) is abundant at low coverage likely associated with isolated molecules or dimers. The zwitterionic phase (HSCH2CH(NH3+)COO-) is largely dominant as the coverage approaches the monolayer limit and is related to the formation of ordered self-assembled molecular structures indicated by electron diffraction patterns. The occurrence of a small amount of cationic molecules (HSCH2CH(NH3+)COOH) is also discussed. The second-layer molecules mainly display zwitterionic character and are weakly adsorbed. Mild annealing up to 100 degrees C leads to the desorption of the second-layer molecules leaving electronic states of the first layer unaltered.