The health burdens of climate change are spread disproportionately, with developing countries being the most affected. These effects burden children in developing countries. This study assesses the effects of climate change on the health of children in parts of Southwest Nigeria, analyzes inter and intra-city variations in the prevalence of climate-related diseases among children, and examines the influence of demographic variables on the incidence pattern. Hospital records of 7,458 children and climatic data of three cities were employed. The results show that 58% of the cases were for female children, while 56% of the diagnosis was for malaria. Other diseases found included diarrhoea (16%), meningitis (6%) and asthma (4%). Temperature and rainfall accounted for 32.3% and 44.6% of the variations in malaria and diarrhoea cases and there were significant inter-city and intra-city variations in the disease incidence. More female children were affected irrespective of their socioeconomic background while 72.2% of children affected were aged below 5.