Malaria remains one of the major public health problems for children in Guinea-Bissau and the major reason for using the health services. Little is known about factors with impact on whether the mothers seek malaria treatment for their children at a health centre. Mothers of children coming to the Bandim Health Centre in Bissau and age-matched controls selected from the registration system of the Bandim Health Project were interviewed about treatment habits, socio-economic standards and other factors associated with the mother seeking treatment for her child at a health centre. In a multivariate analysis, the controls were more often found to have chloroquine at home and had more often taken home treatment for suspected malaria. On average 2.97 persons among cases shared bed as opposed to only 2.02 among controls, bed-crowding thus, being a factor determining health seeking behaviour (P=0.0001). Low socio-economic status, as measured by the non-availability of electricity, was also a significant predicting factor (P=0.02). The possibilities of promoting home treatment should be further evaluated, not only to avoid unnecessary visits to the professional health system, but also to decrease the morbidity from acute malaria.