A capture-recapture study was undertaken to estimate the incidence and likely total burden of malaria cases in England. Cases diagnosed by the national Malaria Reference Laboratory (MRL) between July 2003 and December 2004 were matched with cases reported to Hospital Episode Statistics using demographic, geographical, parasitological, and temporal information. A total of 3861 cases were recorded in one or both datasets; the 'unknown population' was estimated as 746 cases (95% CI 677-822) giving a total of 4607 cases (95% CI 4446-4767) over 18 months. Eighty-four percent (95% CI 83-85) of cases were recorded in one or both datasets. Fifty-six percent (95% CI 54-58) of cases were captured by the MRL surveillance system; ascertainment for Plasmodium falciparum and London cases was higher at 66% and 62%, respectively. Improving case ascertainment will facilitate effective measures to reduce the burden of this preventable disease in the UK.