Primary cilia are microtubule-based organelles mediating sensory and neuroendocrine signaling. The importance of cilia function is underscored by ciliopathies often presenting clinical manifestations such as obesity. Many neurons possess primary cilia that are enriched for certain G protein-coupled receptors, including melanin-concentrating hormone (MCH) receptor 1 (MCHR1). The MCH system is known to mediate distinct aspects of energy balance and vital behavior. Although short cilia have been observed in genetic obese mice, a possible correlation between MCHR1-positive neuronal cilia length and energy metabolism has not been characterized. Here, we established a novel protocol to detect ciliary receptors in rat hippocampal slice culture. Ciliary MCHR1 were abundantly located in the CA1 and CA3 but not in DG. The features in each region were not uniform; the length of ciliary MCHR1 in CA1 were significantly longer than that in the CA3. Then, by using our culture system, we provide the first evidence that endogenous MCHR1-positive cilia length in neuron is significantly reduced by MCH at nanomolar order, and this appears to selectively occur in CA1 neurons. Future work will investigate the molecular mechanism of cilia shortening in responses to MCH.