Systems and methods for providing for the automatic instrument-based rapid reprocessing of an intact extracorporeal circuit for use in hemodialysis. The system includes a manifold with connectors for engaging a dialyzer as well as venous and arterial blood lines. The manifold is adapted to be moved from a dialysis machine to a reuse instrument without removing the dialyzer and associated blood lines. The system allows for reprocessing of the extracorporeal circuit wherein prior to the next treatment, there is no residual chemical disinfectant requiring testing, the extracorporeal circuit is pre-primed, the levels in the bubble traps are set, and all of the required quality assurance tests are performed and recorded.