As part of a 4-year control programme beginning in 2003 and entitled Piga Vita Kichocho, around 140,000 school-aged children on Unguja Island, Zanzibar were treated annually with a combination of praziquantel and albendazole. To provide information on the impact of this intervention, a subset of children, originating from 24 sentinel schools, were monitored in 2004, 2005 and 2006 using both parasitological and behavioural questionnaire methods. Overall, prevalence of urinary schistosomiasis fell by 52%, intensity by 55% and gross haematuria by 82%. There was a positive and statistically significant correlation between areas of elevated disease prevalence and areas of predicted high transmission based upon local occurrence of the permissive intermediate snail host. In areas of low transmission, urinary schistosomiasis was greatly reduced, but, by contrast, other intervention strategies are needed to complement and synergise with chemotherapy in high transmission areas. Whereas significant reductions were documented in the prevalence of both Trichuris trichiura and hookworm, prevalence of Ascaris lumbricoides significantly increased over the monitoring period. Through a detailed analysis of named child records, evidence of predisposition to helminth (re)infection and individual bias towards polyparasitism was detected, highlighting the often overlapping distribution of these parasites within the school-aged child.