Abstract Background The diagnosis of human anaplasmosis remains elusive and is probably often missed. This case report highlights the efficacy of molecular diagnostic techniques. Case presentation We would like to report the case of a 74-year-old man who was admitted to hospital because of a high fever, marked chills, transient diplopic images and vertigo, 6 weeks after multiple tick bites. The laboratory results showed mild anemia, marked thrombocytopenia and leukopenia and a moderately elevated C-reactive protein. The initial serology seemed to indicate an active infection with Borrelia spp., and Anaplasma phagocytophilum was detected in peripheral blood by polymerase chain reaction (PCR) and subsequent sequencing. The patient received intravenous ceftriaxone for 14 days and oral doxycycline for 4 weeks and made a fast and complete recovery. Conclusions While human anaplasmosis has been reported very rarely in Austria, it should be considered as a differential diagnosis in febrile patients with low leukocyte and platelet counts with elevated levels of C-reactive protein after exposure to tick bites. Molecular detection of A. phagocytophilum is the technique of choice allowing rapid and reliable diagnosis.