Classical immunological research investigates immune defense mechanisms in a controlled environment with a narrow genetic diversity and high reproducibility. Aiming the understanding of host immune variations and disease susceptibility in the broad framework of evolution, ecology and life-history, the field of eco-immunology is expanding the focus under the influence of high genetic diversity and abiotic and biotic factors in wild animals. Moreover, immunological research in non-model species is facing methodological challenges by lack of reagents and annotated genomes. Limited by experimental approaches that can easily be used under field conditions eco-immunological research focus mainly on innate and only partially on adaptive immunity. Despite the recent availability of high-throughput technologies, little is known about the development and processes of acquired immunity and how interactions with innate immune cells affect systemic immune responses. In my thesis I focused these issues using chiropteran species which represent an ideal model for eco-immunology due to their high diversity, physiological peculiarities and their prominent role as natural reservoir for pathological viruses.