Diarrhoea, cough and fever are the leading causes of childhood morbidity and mortality in sub-Saharan Africa. Despite it being a determinant of mortality in many developing countries, geographical location has seldom been considered as an explanatory factor for the large regional variations seen in the childhood morbidity attributed to these causes in this area. The relevant data collected in two Nigerian Demographic and Health Surveys, one in 1999 and the other in 2003, have now therefore been analysed and compared. The aim was to reveal and explore inequalities in the health of Nigerian children by mapping the spatial distribution of childhood morbidity associated with recent diarrhoea, cough and fever and accounting for important risk factors, using a Bayesian geo-additive model based on Markov-chain-Monte-Carlo techniques.Although the overall prevalences of recent diarrhoea, cough and fever recorded in 1999 (among children aged ,3 years) were similar to those seen in 2003 (among children aged ,5 years), the mapping of residual spatial effects indicated that, in each survey, the morbidity attributable to each of these causes varied, differently, at state level. Place of birth (hospital v. other), type of feeding (breastfed only v. other), parental education, maternal visits to antenatal clinics, household economic status, marital status of mother and place of residence were each significantly associated with the childhood morbidity investigated. In both surveys, children from urban areas were found to have a significantly lower risk of fever than their rural counterparts. Most other factors affecting diarrhoea, cough and fever differed in the two surveys. The risk of developing each of these three conditions increased in the first 6-8 months after birth but then gradually declined. The analysis explained a significant share of the pronounced residual spatial effects. Maps showing the prevalences of diarrhoea, cough and fever in young children across Nigeria were generated during this study. Such maps should facilitate the development of policies to fulfil the Millennium Development Goals in Nigeria and throughout sub-Saharan Africa.