Objective: To investigate cortical-lumbar-anorectal neural pathways in patients with functional constipation (FC) and to explore potential neural mechanisms in FC. Methods: Sixty cases of FC patients and twenty five healthy controls were enrolled in the study. FC group included 28 males and 32 females,mean age was (49.44 ± 15.38) years;normal control group included 11 males and 14 females,mean age was (24.67 ± 7.14) years. Anorectal motor evoked potentials(MEPs) were recorded following transcranial magnetic stimulation (TMS) over motor cortices and lumbar nerve root bilaterally. Results: ①TMS-MEP results:MEP amplitude in the FC group was significantly lower,and the differentiation of wave form and reproducibility were worse than those in the control group(P < 0.05),but latency and peak-interval changes were not changed significantly. The comparison of bilateral parameters showed no significant difference in both the FC group and the control group. ②MS-LMEP results:In the FC group,evoked potential latency was prolonged and amplitude was significantly lower than the control group(P < 0.05). Conclusion: Cortex-lumbar-anorectal nerve pathway conduction disturbances may be the potential onset FC neurophysiological mechanisms.