The ISIS 800 MeV proton synchrotron presently provides 2.5×1013protons per pulse at 50 Hz, corresponding to a mean power of 160 kW. A dual harmonic RF system upgrade, now being installed, is expected to increase the intensity and power to about 3.75×1013ppp and 240 kW respectively. This paper describes work presently underway to understand and optimise beam loss control, which is a dominant factor determining operational performance. The main features of the collimation system are described, and Monte Carlo simulations of the loss control process are used to understand variations of efficiency with beam loss mode (growth rate, plane). Results of simulations are compared with measurements and operational data. Improvements to measurements are also outlined. © 2003 American Institute of Physics