Serotonergic systems, their phylogeny and ontogeny have been thoroughly described up to the ultrastructural level, thanks to the multiplicity of methodological approaches. They have often been referred to as a 'Rosetta stone', as several features first described for serotonin neurons or paraneurons have been then extended to other neurotransmitter systems: coexistence with neuropeptides or even a canonical neurotransmitter (GABA), volume transmission, regrowth after lesioning, and characterization of multiple receptor subtypes. This review deals with the contributions of neuroanatomical approaches for studying serotoninergic systems, and focuses on recent advances concerning the topological relationships between serotonergic innervation, receptors and target cells. This aspect is particularly important with regard to the possibility for serotonin to act through classical synaptic transmission and/or non-junctional transmission. Serotonin then can selectively regulate different neuronal systems through the activation of distinct receptor subtypes, which in turn can be linked to different transduction pathways. Neurocytochemical approaches constitute unique tools to analyse both anatomical and functional characteristics of complex neuronal systems.