The protozoan parasite Histomonas meleagridis is the causative agent of histomonosis in gallinaceous birds. In turkeys, the disease can result in high mortality due to severe inflammation and necrosis in caecum and liver, whereas in chickens the disease is less severe. Recently, experimental vaccination was shown to protect chickens and turkeys against histomonosis but dynamics in the cellular immune response are not yet demonstrated. In the present work, different groups of birds of both species were vaccinated with attenuated, and/or infected with virulent histomonads. Flow cytometry was applied at different days post inoculation to analyse the absolute number of T-cell subsets and B cells in caecum, liver, spleen and blood, in order to monitor changes in these major lymphocyte subsets. In addition, in chicken samples total white blood cells were investigated. Infected turkeys showed a significant decrease of T cells in the caecum within one week post infection compared to control birds, whereas vaccination showed delayed changes. The challenge of vaccinated turkeys led to a significant increase of all investigated lymphocytes in the blood already at 4 DPI, indicating an effective and fast recall response of the primed immune system. In the caecum of chickens, changes of B cells, CD4(+) and CD8α(+) T cells were much less pronounced than in turkeys, however, mostly caused by virulent histomonads. Analyses of whole blood in non-vaccinated but infected chickens revealed increasing numbers of monocytes/macrophages on all sampling days, whereas a decrease of heterophils was observed directly after challenge, suggesting recruitment of this cell population to the local site of infection. Our results showed that virulent histomonads caused more severe changes in the distribution of lymphocyte subsets in turkeys compared to chickens. Moreover, vaccination with attenuated histomonads resulted in less pronounced alterations in both species, even after challenge.