Airborne pathogens can cause infections within parrot (Psittaciformes) and pigeon (Columbiformes) holdings and, in the case of zoonoses, can even spread to humans. Air sampling is a useful, noninvasive method which can enhance the common sampling methods for detection of microorganisms in bird flocks. In this study, fecal and air samples were taken from four parrot holdings. Additionally, cloacal and oropharyngeal swabs as well as air samples were taken from 15 racing pigeon holdings. Parrots were examined for psittacine beak and feather disease virus (PBFDV), proventricular dilatation disease virus (PDDV), adenoviruses (AdVs), avian paramyxovirus type-1 (APMV-1), avian influenza virus (AIV), Chlamydia psittaci (CP), and Mycobacterium avium complex (MAC). MAC and AdVs were detected in three parrot holdings, CP was detected in two parrot holdings, and PBFDV and PDDV were each detected in one parrot holding. Pigeons were examined for the pigeon circovirus (PiCV), AdVs, and CP; PiCV and AdVs were detected in all investigated pigeon holdings and CP was detected in five pigeon holdings.