The first proton therapy patient was successfully treated for astrocytoma using a modified nuclear experimentation beam line and in‐house treatment planning in 1993. In 1998, IUCF constructed an eye treatment clinic, and conducted a phase III clinical trial investigating proton radiation treatment of AMD. Treatment was planned using Eyeplan modified to match the IUCF beam characteristics. MPRI was conceptualized in 1996 by a consortium of physicians and physicists. Reconfiguration began in 2000; construction of the achromatic trunk line began in 2001, followed by manufacture of 4 energy selection lines and two fixed horizontal beam treatment lines. Two isocentric, rotational gantries will be installed following completion of the horizontal beam lines. A fifth line will supply the full‐time radiation effects research station. Standard proton delivery out of the main stage is specified at 500 nA of 205 MeV. Clinic construction began in April, 2002 and will be completed by mid‐December. Design, construction and operation of these proton facilities have been accomplished by the proton therapy group at IUCF. © 2003 American Institute of Physics