Macrorhabdus ornithogaster is a yeast organism that infects multiple species of captive and wild birds. Diagnosis of infection in vivo has proven difficult historically, as shedding can be intermittent, and not all positive animals are clinically ill. We compared polymerase chain reaction (PCR) of cloacal swab samples and fecal Gram's stain (FGS) for diagnosis of active shedding of M ornithogaster in a captive flock of budgerigars (Melopsittacus undulatus). Of the 100 birds sampled, 57 (57%) were positive for M ornithogaster by PCR and 24 (24%) were positive for M ornithogaster by FGS. All FGS-tested birds also were positive on PCR. There was a significant association between the two methods, but the overall percent agreement for the two methods was only 67%. Based on these findings, cloacal swab PCR is more likely to diagnose the presence of M ornithogaster than FGS in budgerigars.