The uniformity of GaAs, AlAs, and InAs grown in an Intevac/Varian Gen II molecular beam epitaxy system has been characterized using a quantum well (QW) structure and room-temperature photoluminescence (PL) evaluation. Artifacts in the measured distributions have been identified through simulations and were proposed to originate from incomplete rotation averaging during growth of the QW and/or oscillations of the Al mole fraction in the growth direction. The first effect is an actual thickness variation while the second effect leads to shifts in the PL signal that will be incorrectly interpreted as thickness variations when Schrodinger’s equation is solved for wells with symmetric potential barriers. Modeling of the flux distribution predicted that an upward tilt of the substrate away from the group III cells is beneficial. This was confirmed experimentally with the best overall uniformity achieved for a tilt of approximately 9 deg.