We investigated the relationship between abnormal vitamin A cytology and mortality in infants less than 9 months of age with measles. In a 12-month period, 116 children of this age with measles consecutively admitted to Queen Elizabeth Central Hospital (QECH) in Blantyre, Malawi were enrolled in the study. All guardians of patients were interviewed and clinical information and consent were obtained in a standardised fashion. Conjunctival impression cytology (CIC) was attempted on all and collected from 93 (80%) children. The overall mortality was 16%. The proportional hazards model revealed that the presence of pneumonia on admission (hazard ratio 9.58, p = 0.0002) and an abnormal vitamin A CIC on admission (hazard ratio 6.40, p = 0.003) were independently associated with mortality. Our findings suggest a relationship between abnormal vitamin A CIC and fatality in infants under 9 months of age.