Mortality data collected from 1984 to 1987 through a routine standardized health information system in the five main refugee populations of Honduras were reviewed. The direct standardized mean annual death rate for all refugees was 5.5 per 1000 population (Honduras population as reference; Honduras mortality rate: 10.1 per 1000). Mortality decreased or remained stable among Salvadoran refugees from 1984 to 1987, but increased among Nicaraguan refugees after 1985. The highest neonatal (56.1 per 1000 livebirths), infant (126.1 per 1000 livebirths) and under-five-year-olds (35.7 per 1000 child less than five years of age) mortality rates were observed in the two Nicaraguan camps. These two camps had the highest rate of newly arriving refugees. Deaths in infants and under-five-year-olds accounted for 42 and 54.1% of all deaths respectively. Of all deaths under five years of age, respiratory infections, diarrhoeal diseases and measles accounted for 21.4%, 22.1% and 4.7%, respectively. Mortality rates, particularly among under-five-year-olds and infants increased when the rate of newly arriving refugees was higher. The importance of adapted health surveillance in refugee settlements is discussed.