Histomonas meleagridis, a flagellated protozoan parasite, is the causative agent of histomonosis (syn. histomoniasis, blackhead) in turkeys and chickens. The organs primarily affected by the parasite are the caeca and the liver. Until now, only few reports exist in which the parasite has been diagnosed in tissues other than those mentioned above. Hence, the aim of this study was to perform a systematic investigation of various organs of turkeys and specified pathogen-free chickens following an experimental infection with a mono-eukaryotic culture of Histomonas meleagridis in order to determine the dissemination of the flagellate in infected birds. Molecular methods like PCR and in situ hybridization were used for this purpose. For the first time, the DNA of the parasite could be detected in 13 different organs of infected turkeys by PCR including the proventriculus, duodenum, jejunum, caeca, pancreas, bursa of Fabricius, liver, kidney, spleen, heart, lung, thymus and the brain. Most of these findings were further confirmed by in situ hybridization. In contrast to the turkeys that all died shortly after the infection, all of the chickens survived without displaying any clinical symptoms. Even at necropsy, only mild pathological changes were observed in the caeca. Nevertheless, the parasite could also be detected in various organs of these birds, namely the caeca, bursa of Fabricius, kidney, heart and the brain.