Objective To study whether the expression of serotonin (5-HT) and serotonin transporter (SERT) in the dorsal raphe nucleus (DRN) and caudate putamen (CPu) are altered in Parkinsonian rats induced by rotenone. Methods Forty-two healthy, adult male Wistar rats were divided into the rotenone-treated (21 rats) and the control (21 rats) groups. Rotenone was injected subcutaneously in the back of the rat to establish a Pakinsonian model. Immunocytochemistry, Western blotting and flow cytometry were used to analyze the expression of 5-HT and SERT in the brains of the rats treated by rotenone. Results 1. Immunocytochemistry showed that the number of 5-HT immunoreative positive neurons in DRN was less in rotenone treated rats than in the control (EM>P/EM><0.01), the immunoreactive intensity of 5-HT in DRN and CPu was weaker in the rotenone treated rat than in the control (EM>P/EM><0.01); Flow cytometry showed that the expression of 5-HT in the rotenone treated rats decreased significantly compared to the control (EM>P/EM><0.01). 2. Immunocytochemistry showed the immunoreactive intensity of SERT in CPu was weaker in the rotenone treated rat than that in the control (EM>P/EM><0.01); Western blotting showed the ratio of SERT/β-actin in the rotenone treated rat was lower than in the control (EM>P/EM><0.05). Conclusion Rotenone bears obvious toxicity to serotone