Aspergillosis is the most important disease in hunting/racing falcons in the Middle East. Based on clinical observations, the gyrfalcon (Falco rusticolus) is considered to be more susceptible than other species of falcons, whereas it has been hypothesized that their hybrids might be more resistant. This retrospective study examined the endoscopic results of 3,754 captive-bred juvenile falcons of three different species and their hybrids, admitted to Dubai Falcon Hospital in their first year in the UAE over a 14-year period. A control cohort of confirmed genetic origin from Dubai Falcon Center was also examined. Aspergillosis was diagnosed in 887 falcons. The overall prevalence, regardless of species, was 24%. Gyrfalcons (F. rusticolus) had a prevalence of 27%, peregrine falcons (Falco peregrinus) of 18%, and saker falcons (Falco cherrug) of 26%. There was no significant difference in the prevalence of aspergillosis between the total hybrid population and the total purebred population. Among purebreds, there was a statistically significant difference only between gyrfalcon and peregrine falcon, with the gyrfalcon being more sensitive. Additionally, the gyrfalcon had a statistically higher prevalence of aspergillosis than the total population of gyrfalcon hybrids. The most resistant hybrid proved to be the gyrfalcon × peregrine (prevalence 20%). This was also verified in the Dubai Falcon Center cohort. In assessment of two main gyrfalcon hybrids in accordance with their parental ancestors, the gyrfalcon–peregrine hybrid proved to be more resistant than the gyrfalcon ancestry, but not the peregrine ancestry. The gyrfalcon–saker presented numerically higher prevalence (30%) than both parents (gyrfalcon, saker falcon), showing outbreeding depression. There was no statistically significant difference between captive-bred sakers (prevalence 24%) and legally harvested wild-caught sakers from Mongolia (prevalence 26%). This work partially confirmed the clinical hypothesis of gyrfalcon sensitivity and hybrid superiority regarding aspergillosis prevalence, only in relation to the peregrine falcon and the gyrfalcon–peregrine hybrid.