A system and method for treating anorectal dysfunction includes implanting, in a minimally invasive manner, an electro-medical device for stimulation of two or more separate and distinct anatomical or histological structures of the anorectal region. Electrodes operably connected to the device are positioned proximate the target anatomical or histological structures. The device provides either the same or different stimulation algorithms to each anatomical or histological structure. Smooth muscle, such as the internal anal sphincter, is provided with a continuous stimulation algorithm, while skeletal muscle, such as the external anal sphincter, is provided with an on demand stimulation algorithm. Varying stimulation algorithms applied to multiple structures results in improved anorectal function without developing muscle fatigue and tolerance.