Abstract Background Recently the financial status of primary care trusts has come under considerable scrutiny by the government, and financial deficits have been blamed on poor local management of resources. This paper examines the factors that differ between those Primary Care Trusts (PCT) in financial deficit and those in surplus, using readily available data at PCT level. PCTs are the National Health Service organisations in England responsible for improving the health of their population, developing primary and community health services, and commissioning secondary care services. Methods A descriptive comparative study using data from 58 PCTs; 29 in greatest financial surplus and 29 in greatest deficit in the English National Health Service. Results Nearly half the study deficit PCTs (14 out of 29) are in the East of England and of the 29 surplus PCTs, five each are in Birmingham and Black Country Strategic Health Authority (SHA), and Greater Manchester SHA. The median population density of the deficit PCTs is almost seven times lower than that of surplus PCTs (p = 0.004). Surplus PCTs predominantly serve deprived communities. Nearly half the surplus PCTs are 'spearhead' PCTs compared to only one of the deficit PCTs. Percentage population increase by local authority of the PCT showed that on average deficit PCTs had 2.7 times higher change during 1982–2002 (13.37% for deficit and 4.94% for surplus PCTs). Work pressure felt by staff is significantly higher in deficit PCTs, and they also reported working higher amount of extra hours due to work pressures. The proportion of dispensing general practitioners is significantly higher in deficit PCTs 40.5% vs. 12.9% (p = 0.002). Deficit PCTs on average received £123 less per head of registered population compared to surplus PCTs. Conclusion The two groups of PCTs serve two distinct populations with marked differences between the two. Deficit PCTs tend to be in relatively affluent and rural areas. Poor management alone is unlikely to be the cause of deficits, and potential reasons for deficits including rurality and increased demand for health services in more affluent communities need further in-depth studies.