The objective of this study was to verify the accuracy of the quantitative PCR (qPCR) method for in vivo detection of Macrorhabdus ornithogaster. A total of 100 faecal and gastric mucosa samples from avian cadavers were investigated, using cytological and qPCR techniques (budgerigars, Fischer's lovebirds, red-crowned parakeets, scarlet-chested parrots, eastern rosellas, domestic canaries, zebra finches, white Java sparrow). Using qPCR, the probability of detecting positive samples of droppings was significantly higher than in the faecal smear microscopy (P < 0.01). Cytology detected the presence of Macrorhabdus ornithogaster in 34 faecal samples, whereas qPCR detected 54 positive samples. In all 46 qPCR negative faecal samples, gastric smear qPCR was performed and also yielded negative results. Gastric smear qPCR was also performed in 20 cadavers where faecal qPCR has detected the presence of Macrorhabdus ornithogaster and in all samples confirmed the positive result. This verifies the accuracy of faecal sample qPCR for intravital diagnostics. Overall, the faecal qPCR technique appears to be extremely reliable, as it made it possible to detect all infected individuals, including those with negative stool or gastric cytology.