The first paramyxovirus termed BatPV/Myo.mys/E20/09 was detected in pooled organs and was subsequently confirmed in the kidney only of one adult male whiskered bat (Myotis mystacinus) found in Bavaria. Histological examination of the internal organs revealed multifocal mild interstitial nephritis with lymphoplasmacytic infiltrates and occasional neutrophiles. Lungs had mild nonsuppurative interstitial pneumonia and marked leucocytostasis in most blood vessels. Additionally, there was distinct activation of the lymphoreticular tissue of the spleen with moderate follicular hyperplasia and sparse irregularly distributed small foci of lymphocytes and plasma cell aggregations within the liver.