We studied the incidence and clinical associations of hypoglycaemia in an acute medical paediatric service in Maputo, Mozambique. Of 603 children, 43 (7.1%) were hypoglycaemic. 16 of these with Plasmodium falciparum malaria had a shorter illness, and a higher incidence of convulsions and focal neurological signs than those with other diagnoses, but were less likely to die. Hypoglycaemia also complicated protein energy malnutrition, pneumonia, encephalitis, intestinal parasite infection, and nephrotic syndrome. 25 of the 603 children died: 7 (16.3%) of 43 with hypoglycaemia and 18 (3.2%) of 560 who were normoglycaemic, (relative risk of death 5.8 [95% confidence interval 2.25 to 14.93]). Hypoglycaemia is common in children in hospital in Mozambique, and should be suspected in any acutely-ill child regardless of the primary disease.