Allergy testing is an important pre-requisite for both early identification of infants at increased risk for later development of allergic diseases and for specific allergy treatment including specific allergen avoidance measures, pharmacotherapy and specific immunotherapy. The aim of this study was to investigate the influence of in vitro allergen-specific immunoglobulin E (IgE) testing on the primary care physician’s diagnosis and clinical management of children with symptoms of eczema, wheezing/asthma and rhinitis. The trial was a prospective study performed at 14 paediatric primary care practices in Germany, covering 380 children below 6 yr of age. For one group of children the physician received the IgE test results as soon as possible and used them as an additional tool when diagnosing and giving clinical management advice. For the other group of children the IgE test results were not made available to the physician until the children were brought to a second visit, about 7 wk later. When diagnosis was made without access to allergen-specific IgE results, 8% of the children were diagnosed as allergic, 6% as non-allergic and in 86% of the cases the physician was uncertain. With access to allergen-specific IgE results the figures were 13%, 65% and 22%, respectively. Concerning clinical management advice no statistically significant differences between the two study groups were observed. When comparing the first and second visits of the patients coming for a second visit advice to reduce aeroallergen exposure was given to 27% of the patients at visit 1 and to 36% of the patients at visit 2 (p = 0.002). The difference between the first and second visits of the other clinical management advice studied did not reach statistical significance. In this study the availability of IgE test results to the primary care physician had an impact on the decision-making process of the diagnosis but not on the pharmaceutical or avoidance advice given. The reason why IgE test results were not fully exploited needs to be further scrutinized.