Neuroinflammation seems to be involved in the pathophysiology of Huntington’s Disease (HD), but its specific role on different stages of the disease, especially in later stages, remains to be understood. Here in, we investigated the concentrations of cytokines, chemokines and neurotrophic factors in striatum and frontal cortex of 24-month-old BACHD mice, a murine model of that displays several behavioral and pathological features of human HD. Our results revealed increased concentrations of the chemokine MCP-1 and the neurotrophin NGF in the striatum of BACHD mice alongside a reduction in the levels of the cytokine IL-6 and of the neurotrophin BDNF. In the frontal cortex, we found decreased levels of BDNF and MCP-1. We provide the first evidence that cytokines and neurotrophic factors may contribute to the pathophysiology of advanced HD.