After some well-publicised problems with paediatric cardiac surgery, there has been great interest in England in monitoring clinical quality in specialised medical services. The National Commissioning Group plans, funds and monitors a set of highly specialised services for the National Health Service in England. We have developed systems for monitoring clinical quality that perform two interrelated but distinct functions: performance measurement and performance improvement. The aim is to collect information on all patients seen during each year--a 100% consecutive case series. Generally, there is no conceptual difficulty identifying an appropriate outcome for surgical interventions: the indication for surgery usually defines the outcome to monitor. This is not so for the medical and psychiatric services, where the relevant outcome to monitor is sometimes not obvious. There are a number of problems in interpreting, and acting on, outcome data for rare conditions and treatments. These problems include statistical problems due to small numbers, the need to risk adjust data and coding problems.