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White stork (Ciconia ciconia) chicks have previously been suggested to be particularly susceptible to environmental conditions such as climatic changes during their first 3 wk of life. However, limited data are available on causes of mortality in free-ranging birds prior to fledging in general. One hundred and one white stork chicks found dead in 2007 and 2008 were examined and the causes of death identified. Of these, 44.6% had fungal granulomatous pneumonia resulting in obstruction and compression of airways. Of note, 94.1% of pulmonary infections occurred in white stork chicks below 23 days of age. PCR amplification and sequencing of the fungal internal transcribed spacer region 1 identified Aspergillus fumigatus and various zygomycetes as primary causative agents. Thermomyces lanuginosus, previously unknown to cause pulmonary infections, was identified in one chick. The findings suggest that fungal pneumonia plays a major role in the loss of white stork chicks of up to 3 wk of age and represents a major threat, similar to the threat posed to young poultry.