A total of 110 sites from five zoological institutions were examined to determine whether fungi associated with sick building syndrome (SBS) were prevalent in the exhibits or night-time holding facilities and to investigate whether the presence of these organisms was associated with declining breeding rates or increases in morbidity and mortality (or both). Each site was sampled with an Andersen two-stage air sampler using Sabourauds dextrose agar media and a Burkard personal volumetric air sampler. Suspect surfaces were also sampled. High levels of airborne Penicillium chrysogenum, a fungal species associated with poor indoor air quality, were recovered from 16 sites out of all five institutions. Five culturable growth sites of Stachybotrys chartarum, a species strongly associated with SBS and commonly known as “black mold,” were recovered from surfaces at two institutions. A wide range of other fungal species was recovered in low numbers from all institutions. A Fisher exact test analysis showed a significant nonrandom association between high levels of P. chrysogenum and sites with records of poor animal health. This study indicated that significant numbers of airborne fungi associated with SBS and poor indoor air quality are present in zoological institutions and that they could affect animal health and reproduction rates and zoo staff.