Background The Quality and Outcomes Framework (QOF) has specific targets for body mass index (BMI) and blood pressure recording in major mental illness (MMI), diabetes, and chronic kidney disease (CKD). Although aspects of MMI (schizophrenia, bipolar disorder, and related psychoses) are incentivised, barriers to care may occur. Aim To compare payment, population achievement, and exception rates for blood pressure and BMI recording in MMI relative to diabetes and CKD across the UK. Design and setting Analysis of 2012/2013 QOF data from 9731 UK general practices 2 years after the introduction of the mental health, BMI, and blood pressure QOF indicators. Method Payment, exception, and population achievement rates for the MMI and CKD blood pressure indicators and the MMI and diabetes BMI indicators were calculated and compared. Results UK payment and population achievement rates for BMI recording for MMI were significantly lower than for diabetes (payment: 92.7% versus 95.5% and population achievement: 84.0% versus 92.5%, P< 0.001) and exception rates were higher (8.1% versus 2.0%, P< 0.001). For blood pressure recording, UK payment and population achievement rates were significantly lower for MMI than for CKD (94.1% versus 97.8% and 87.0% versus 97.1%, P< 0.001), while exception rate was higher (6.5% versus 0.0%, P< 0.001). This was observed for all countries. Compared with England, Northern Ireland had higher population achievement rates for both mental health indicators, whereas Scotland and Wales had lower rates. There were no cross-jurisdiction differences for CKD and diabetes. Conclusion Differences in payment, exception, and population achievement rates for blood pressure and BMI recording for MMI relative to CKD and diabetes were observed across the UK. These findings suggest potential inequalities in the monitoring of physical health in MMI within the UK primary care system.