Clinical outcome of Schistosoma haematobium infection may vary significantly, ranging from mild symptoms to severe damage of urinary tract organs. This present study was undertaken to assess the relationship of a number of epidemiological and parasitological parameters with disease outcome in children from rural Zimbabwe. We surveyed 551 primary school students from three schools in the Chikwaka Communal Lands for schistosomiasis; 59.7% were infected with S. haematobium. Ultrasound examination of 189 of the infected students revealed that 50% had pathological changes of their bladder and 36% had abnormal pyelon dilation of at least one of their kidneys. Intensity of infection, certain water contact behaviours, male gender, proteinuria, and self-perceived haematuria were associated with increased bladder damage. Strenuous playing was negatively associated with pathology, especially for those with the highest grade of bladder damage. Kidney pathology was significantly linked with fatigue and pain upon urination and was more prevalent in students from schools closest to the major river systems. Our findings suggest that pathology due to urinary schistosomiasis is widespread and symptomatic in this population. The associations with bladder and kidney pathology can be used to predict disease severity and may be useful in targeting treatment to those most at risk.