Macrorhabdosis is a debilitating disease condition that affects budgerigars (Melopsittacus undulatus), cockatiels (Nymphicus hollandicus), and many other bird species worldwide. Macrorhabdus ornithogaster is a pathogen which leads to nonspecific clinical signs, and to date, diagnosis as well as therapy are still challenging. In this study, medical histories of 32 budgerigars and 7 cockatiels with macrorhabdosis diagnosed clinically and by polymerase chain reaction (PCR) within a period of 24 months (from January 2016 to January 2018) were retrospectively analyzed. Macrorhabdus ornithogaster was diagnosed through fecal samples collected over several days and analyzed by microscopic examination or PCR. The effectiveness of 2 different amphotericin B treatment regimens were investigated by PCR. In 23 cases, treatment was performed with amphotericin B via drinking water at 0.1 mg/mL for 28 days. For the remaining 16 birds, an alternative treatment regimen of amphotericin B at 100 mg/kg PO q12h for 10 days was combined with administration of amphotericin B via drinking water at 0.1 mg/mL for 28 days. Fecal samples of all treated flocks were reexamined by PCR 10–14 days post-amphotericin B treatment. More than half (56.4%) of the treated birds tested negative for M ornithogaster irrespective of the treatment regimen. In addition to clinical improvement and microscopic examination of droppings, PCR was used for the first time to evaluate treatment response in birds diagnosed with M ornithogaster. Administration of amphotericin B via drinking water proved to be effective in more than 50% of cases, indicating a less stressful alternative to the oral administration of amphotericin B twice daily.