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Abstract Background Histomonosis, caused by the protozoan parasite Histomonas meleagridis, is a severe disease especially in turkeys where it can cause high mortalities. Recently, outbreaks were described in which turkey hens showed no clinical signs despite high mortalities in toms, from which they were separated only by a wire fence. The present study investigated three similar outbreaks of histomonosis whereby in two of them only a few hens were being affected and none in the third. Hens from all flocks were kept until end of production and slaughtered as scheduled. However, in all three cases, the disease progressed in toms reaching nearly 100% within two weeks. Methods Following diagnosis of the disease, tissue samples were obtained from toms and hens at necropsy. Environmental dust, cloacal swabs and blood were taken on three successive farm visits within compartments of hens and toms and tested by real-time PCR or ELISA. The DNA from a total of 18 samples positive for H. meleagridis was further subjected to conventional PCR utilizing the 18S rRNA primers and sequenced for phylogenetic analysis. Results All tissue samples and some cloacal swabs were tested positive. Dust samples confirmed the presence of H. meleagridis DNA that spread within entire houses up to 6 weeks after the first clinical signs of histomonosis. Sequence analysis of the 18S rRNA locus demonstrated the presence of the same strain in birds of both sexes within each of the turkey houses. Investigation of serum samples two weeks post-initial diagnosis and prior to euthanasia resulted in antibody detection in 73% of toms and 70% of hens. Until the end of the investigation the number of positive hens per farm increased up to 100% with mean OD-values approaching those noticed in toms prior to euthanasia. Conclusions For the first time it could be demonstrated that turkey hens kept in the same house as toms became infected during fatal outbreaks in toms. This highlights the value of different diagnostics methods in order to trace the parasite in connection with the host response. The strange phenomenon that only single hens succumb to the diseases despite being infected requires further investigations.