Background: Individuals living in Schistosoma haematobium endemic areas are often at risk of having other communicable diseases, simultaneously. This usually creates diagnostic difficulties leading to misdiagnosis and overlooking schistosomiasis infection. In this study we investigated the prevalence and effects of coinfections in pre-school age children and further investigated association between S. haematobium prevalence and under 5 mortality.Methods: Four hundred and sixty five Preschool age children (1-5 years old) with 51% being male were clinically examined for the following top morbidity causing conditions: respiratory tract infections, dermatophytosis, malaria and fever of unknown origin. The conditions were diagnosed as per approved WHO standards. S. haematobium infection was diagnosed by urine filtration and the children were screened for conditions common in the study area which included HIV, tuberculosis, malnutrition and typhoid. Results: Prevalence of S. haematobium was 35% (145). The clinical conditions assessed had the following prevalence in the study population: upper respiratory tract infection 40% (229), fever of unknown origin 45% (189), dermatophytosis and malaria both had 18% (75), The odds of co-infections observed with S. haematobium infection were: upper respiratory tract infection AOR = 1.22 (95% CI 0.80 to 1.87), dermatophytosis AOR = 4.79 ( 95% CI 2.78 to 8.25), fever of unknown origin AOR = 10.63 ( 95% CI 6.48-17.45) and malaria AOR = 0.91 ( 95% CI 0.51 to1.58). Relative risks of the severe sequels when coinfected were: Severe pneumonia RR=7.5 (95% CI 2.92-19.23), p<0.0001, complicated malaria RR=12 (95%CI 11.53-94.53), p=0.02, severe dermatophytosis RR=8.5 (95% CI 1.2-60.2):p=0.03, and fever of unknown origin RR=2.32 (95% CI 1.12-4.80), p=0.02.Conclusion: This study is novel as it identifies a possible association relationship between S. haematobium infection and top morbidity conditions in children under five years. There is need to alert policy makers so as to initiate early treatment of schistosomiasis in pre-school age children.