Children with traditionally defined cerebral malaria (CM) can be subcategorized by the presence or absence of malaria retinopathy. We retrospectively reviewed the seasonal pattern of retinopathy status in patients admitted with CM in Blantyre, Malawi from 1997 to 2010. The proportion of children with CM who were retinopathy-positive was significantly greater during the peak seasonal rains when the community incidence of uncomplicated malaria is higher. This finding supports the hypothesis that retinopathy-negative and retinopathy-positive CM categories have different underlying etiologies.