Thus, this study was meant to meet the following objectives: (i) to compare the motor cortex inhibition indexed by the TMS measures SICI and ICF as well as the DPMS to evaluate the neuroplastic changes in FM, MDD, and HS; (ii) to compare the inhibitory function at the cortical level indexed by the SICI and ICF as well as the descending pain inhibitory system between clinical diagnoses (FM and MDD) considering the BDNF adjusted index as a marker of neuroplasticity; (iii) to examine the relationship between the role of DPMS with the BDNF adjusted index despite clinical diagnosis. This evidence concerns the gene BDNF and major depressive disorder.