Waiting times are of central importance to satisfaction with publicly-funded health care. We explore how the implementation of progressively tight and stringently enforced waiting times targets over the period 2000–2008 in the English NHS and their subsequent relaxing in 2010 affected patient prioritisation for planned treatment. We adopt the Conditional Density Estimation approach to analyse how hospitals respond to waiting time targets and whether the relative ordering of patients is preserved. Our results show that one of the mechanisms for meeting the target is reducing the waiting times for long-waiting patients at the expense of short-waiting patients. We detect statistically significant changes in prioritisation between different groups of patients. A simple explanation for the observed prioritisation patterns based on well-established queuing and scheduling concepts is provided.