In the present investigation flow cytometric analysis and immunohistochemistry were applied together for the first time to gain new insights into the interaction between virulent fowl adenoviruses (FAdV) and the immune system of chickens. As a model for virulent FAdV infections a FAdV-4 strain was used, known as the aetiological agent of Hepatitis-Hydropericardium syndrome (HHS) in broilers sometimes also named Angara Disease. Specified pathogen-free chickens (SPF) were divided into three different groups. Group I was infected at first day of life with an attenuated form of the virus obtained through continuous cell culture passage with the virulent virus and then re-infected 3 weeks later with the virulent progenitor virus. Group II was solely infected with the virulent virus at 3 weeks and group III served as a negative control. Following infection with the virulent virus a decrease of CD3+, CD4+ and CD8+ cells was noticed in the spleen. This was accompanied by a decrease of CD4+ and CD8+ T-lymphocytes in the thymus. Those birds infected with the attenuated virus in first instance and challenged with the virulent virus did not show these pathological effects in the thymus. In the bursa of Fabricius a severe depletion of lymphocytes was observed by immunohistochemistry in birds, infected with the virulent virus. Taken together it can be concluded that an infection with FAdV-4 has profound effects on cells, of the humoral and cell-mediated immune responses. The effects are much more severe in the birds infected with the virulent virus only indicating that the preceding infection with the attenuated virus reduces significantly the adverse effects induced by the virulent virus.