Type 1 allergy against natural rubber latex is an increasing problem in health care workers and children with spina bifida or urogenital malformations. The aim of our study was to evaluate the prevalence of latex IgE antibodies and cross-reacting fruit antibodies in patients with spina bifida compared with atopic and non-atopic controls. Risk factors for sensitization should be determined. Sera of 148 patients with spina bifida and 98 controls (44 with atopy) were screened for IgE antibodies against latex, banana and kiwi by fluorescence enzyme immunoassay (CAP system). Atopies, allergic symptoms after latex contacts and the number of operations were compiled by a questionnaire. Patients with spina bifida developed latex IgE antibodies (≥0.7 kU/l) more frequently (40.5%) than atopic children (11.4%) or healthy controls (1.9%). All 18 symptomatic patients belonged to the spina bifida group and had high values of latex antibodies. The risk for developing latex antibodies increases with the number of operations. There was no difference in the history of atopic diseases and in a screening test of IgE antibodies against inhalative allergens between latex sensitized and not sensitized children with spina bifida. Antibodies against banana were more frequent in the latex sensitized children with spina bifida. (18.3% vs 3.4%, P = 0.002). Conclusion The high prevalence of latex antibodies in children with spina bifida justifies a primary prophylaxis by avoiding latex contacts, especially during anaesthesia and surgery, a correlation between the number of operations and the development of latex antibodies exists.