The basal ganglia are a set of subcortical structures involved in psychomotor behaviour. Parkinson’s disease is the most common neurodegenerative disorder affecting the basal ganglia. The slow and progressive degeneration of dopamine (DA) neurons located in the substantia nigra pars compacta leads to disabling motor symptoms such as bradykinesia, resting tremor and rigidity. This work aims at describing the compensatory mechanisms affecting other neuronal systems and designed to compensate for the massive loss of the DA innervation of the basal ganglia. The thesis begins with a post-mortem human study of the main serotonin (5-HT) pathways arising from the raphe nuclei and innervating the different basal ganglia components in normal condition. The next chapter contains a morphological study providing the first detailed description of single axons arising from the dorsal raphe nucleus (DRN) in rats. In order to achieve our goal, under electrophysiological guidance, microiontophoretic tracer injections of an anterograde tracer were placed in the DRN to provide three-dimensional axonal reconstructions of single 5-HT neurons. Other studies presented were performed in animal models of Parkinson’s disease and brought to light new compensatory mechanisms involving the 5-HT and DA innervation of the basal ganglia. Two articles contain data on major neuroadaptative changes of DA and 5-HT innervation of the striatum and the globus pallidus (GP), following a DA lesion in cynomolgus monkeys (Macaca fascicularis). Immunohistochemistry combined to unbiased quantitative approaches indicate an important sprouting of 5-HT axons in the monkey striatum and GP. Interestingly, in contrast to the massive striatal DA denervation, we report a ten-time increase of the number of DA axons in the GP internal segment of parkinsonian monkeys. Electron microscopy study suggests that the newly-formed 5-HT axon varicosities observed in the striatum establish more synapses after DA lesion, in line with the sprouting of 5-HT axons. The last chapter contains a meticulous morphological study of a peculiar population of medium spiny neurons endowed with a dendritic arborization that is less affected by DA lesion in mice. In summary, studies presented in this doctoral thesis shed a new light on some of the compensatory mechanisms observed in different basal ganglia components and designed to cope for the massive loss of DA neurons that characterize Parkinson’s disease. The compensatory mechanisms outlined in this work should be taken into account to better understand the expression of motor and non-motor symptoms as well as the expression of dyskinesia induced by long-term pharmacological treatment with L-Dopa.