A prospective case-control study was performed in urban and periurban areas of Basel to investigate the epidemiology of Cryptosporidium sp., an intestinal coccidian parasite. 455 children with diarrhoea, who attended paediatric and general practices, participated in the study. Oocysts of the parasite were detected in stool specimens of 21 (4.6%) patients using auramine-fluorescence and modified Ziehl-Neelson staining. Another ten infected people were found during separate investigations of outbreaks in a Kindergarten and in two families. Serial stool stains were performed to determine the period of oocyst shedding. The median duration of diarrhoea was six days and ranged from 1 to 25 days. In contrast, shedding of oocysts of Cryptosporidium sp. lasted for 12.5 days and was significantly longer than the period of diarrhoea (p = 0.02). Compared with control patients suffering from diarrhoea of other origin, respiratory symptoms were significantly (p = 0.02) more frequent in children with cryptosporidiosis (42% vs 13%). In comparison with healthy controls, prior contact with a person suffering from diarrhoea and travel to a Mediterranean country were the most important risk factors for cryptosporidiosis. An illustrative case is described in detail. It is concluded that cryptosporidial infection of the respiratory tract may also occur in immunocompetent children. The possibility of a long period of oocyst shedding is important for the planning of hygiene measures both in individuals and public health.