BACKGROUND: Hypoglycaemia is a frequent complication among admitted children, particularly in malaria-endemic areas. This study aimed to estimate the occurrence of hypoglycaemia not only upon admission but throughout the first 72 h of hospitalization in children admitted with malaria. METHODS: A simple pilot study to continuously monitor glycaemia in children aged 0-10 years, admitted with malaria in a rural hospital was conducted in Southern Mozambique by inserting continuous glucose monitors (CGMs) in subcutaneous tissue of the abdominal area, producing glycaemia readings every 5 min. RESULTS: Glucose was continuously monitored during a mean of 48 h, in 74 children. Continuous measurements of blood glucose were available for 72/74 children (97.3%). Sixty-five of them were admitted with density-specific malaria diagnosis criteria (17 severe, 48 uncomplicated). Five children (7.7%) had hypoglycaemia (<54 mg/dL) on admission as detected by routine capillary determination. Analysing the data collected by the CGMs, hypoglycaemia episodes (<54 mg/dL) were detected in 10/65 (15.4%) of the children, of which 7 (10.8%) could be classified as severe (≤45 mg/dL). No risk factors were independently associated with the presence of at least one episode of hypoglycaemia (<54 mg/dL) during hospitalization. Only one death occurred among a normoglycaemic child. All episodes of hypoglycaemia detected by CGMs were subclinical episodes or not perceived by caregivers or clinical staff. CONCLUSIONS: Hypoglycaemia beyond admission in children with malaria appears to be much more frequent than what had been previously described. The clinical relevance of these episodes of hypoglycaemia in the medium or long term remains to be determined.