A neural stimulation system controls the delivery of neural stimulation using a respiratory signal as a therapy feedback input. The respiratory signal is used to increase the effectiveness of the neural stimulation, such as vagal nerve stimulation, while decreasing potentially adverse side effects in respiratory functions. In one embodiment, the neural stimulation system synchronizes the delivery of the neural stimulation pulses to the respiratory cycles using a respiratory fiducial point in the respiratory signal and a delay interval. In another embodiment, the neural stimulation system detects a respiratory disorder and, in response, adjusts the delivery of the neural stimulation pulses and/or delivers a respiratory therapy treating the detected respiratory disorder.