Intestinal helminths, schistosomiasis and malaria have been recognised for decades to be major public health problems in Zanzibar, Tanzania. During the evaluation of the impact of the Zanzibar Helminth Control Programme, baseline parasitological data on 3,605 school children were collected in Pemba Island. Prevalence of intestinal helminth infections was 72%, 94% and 96% for Ascaris lumbricoides, Trichuris trichiura and hookworm, respectively. Thirty one percent of children tested positive for haematuria, a reliable indicator of urinary schistosomiasis in the study area. Malaria parasites were found in 61% of children. Hookworm infections and haematuria were more prevalent in boys. Sixty seven percent of the children were infected with all the three helminths, and 28% harboured double infection. No association was found between intestinal helminths and schistosomiasis or malaria. Children living in rural areas were more heavily infected with hookworms, schistosomiasis and malaria compared to children in towns. Results from this study provided relevant information for designing a "plan of action" for the integrated control of filariasis, intestinal helminths, malaria and schistosomiasis in Zanzibar.