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Introduction: Usutu virus (USUV) is an emerging mosquito-borne flavivirus. USUV-related outbreaks of disease and mortality in wild birds, as well as neuroinvasive disease in humans have raised a health concern in Europe. Although a few pathologic studies describe the morphologic features of USUV-associated encephalitis in naturally infected wild birds, data regarding the immune response in situ are still lacking. This study aims to characterize the immune-cell populations in Usutu virus-associated encephalitis, comparing uninfected birds with birds infected with two circulating virus lineages. Materials and Methods: Immunohistochemistry was performed with specific antibodies for CD3 (T cells), PAX5 (early B cells) and MUM1 (late B cells and plasma cells) on brain tissue. Cell count was performed, and results were compared between uninfected birds (n = 4) and birds infected with Europe-3 (n = 4) and Africa-3 (n = 4) USUV-lineage. Results: The numbers of T cells and early and late B cells were higher in USUV-infected birds compared with uninfected birds, the majority being CD3+ cells. The PAX5+ cell count was higher, to a small degree, in Africa-3 compared with Europe-3-infected birds. Conclusions: This study reveals a major T cell and a minor B cell involvement in the immunopathology of Usutu virus-associated encephalitis. A slightly higher number of B cells in Africa-3-infected birds suggests a possible difference in the host response to these two lineages. Further and larger scale studies are needed to characterize the T cell population.