Background The world's growing population of asylum seekers faces different health risks from the populations of their host countries because of risk factors before and after migration. There is a current lack of insight into their health status. Methods A unique notification system was designed to monitor mortality in Dutch asylum seeker centres (2002–2005). Results Standardised for age and sex, overall mortality among asylum seekers shows no difference from the Dutch population. However, it differs between subpopulations by sex, age and region of origin and by cause of death. Mortality among asylum seekers is higher than among the Dutch reference population at younger ages and lower at ages above 40. The most common causes of death among asylum seekers are cancer, cardiovascular diseases and external causes. Increased mortality was found from infectious diseases (males, standardised mortality ratio (SMR)=5.44 (95% CI 3.22 to 8.59); females, SMR=7.53 (95% CI 4.22 to 12.43)), external causes (males, SMR=1.95 (95% CI 0.52 to 2.46); females SMR=1.60 (95% CI 0.87 to 2.68)) and congenital anomalies in females (SMR 2.42; 95% CI 1.16 to 4.45). Considerable differences were found between regions of origin. Maternal mortality was increased (rate ratio 10.08; 95% CI 8.02 to 12.83) as a result of deaths among African women. Conclusion Certain subgroups of asylum seekers (classified by age, sex and region of origin) are at increased risk of certain causes of death compared with the host population. Policies and services for asylum seekers should address both causes for which asylum seekers are at increased risk and causes with large absolute mortality, taking into account differences between subgroups.