An implantation device for releasably holding implantable microstimulators can be used to guide one or more microstimulators to any site within the gastrointestinal tract for implantation. The device can further releasably hold one or more ligation clips for securing the one or more microstimulators in place within the implantation site(s) and/or for closing an incision in which a microstimulator is implanted. The device can be employed using open, laparoscopic, and endoscopic techniques.