Background Cytauxzoonosis is gaining clinical importance in recent years, being described as an emerging tick-borne disease of domestic and wild felids caused by protozoans of the genus Cytauxzoon . While in the Americas the condition is described as a fatal disease, in Europe, reports on the clinical expression of the infection are scarce. This study describes the first case of Cytauxzoon sp. infection in a domestic cat in Germany. Methods Clinical and laboratory findings, and molecular and DNA sequencing results were collected from a domestic cat suspected for cytauxzoonosis after the microscopic examination of a blood smear. Results A 6-year-old male domestic cat living in Saarlouis (Germany) was presented with a history of recent anorexia and weight loss. The cat had an outdoor lifestyle and had not travelled abroad. Serum clinical chemistry analysis revealed azotaemia with markedly increased symmetric dimethylarginine, hypercreatinemia, hyperphosphatemia and hypoalbuminemia. Moreover, a mild non-regenerative anaemia was present. Approximately one year prior these findings, the patient was diagnosed with a FIV infection. These results point toward a decreased glomerular filtration rate, presumably as a result of a kidney dysfunction. Therefore, a glomerulonephropathy was suspected. Round to oval signet-ring shaped intraerythrocytic organisms, morphologically suggestive for a piroplasm, were revealed during blood smear evaluation with a degree of parasitaemia of 32.95%. PCR analyses and sequencing of the partial 18S gene confirmed the presence of a Cytauxzoon sp. infection, with 99-100% nucleotide sequence identity with previously published Cytauxzoon sp. isolates. Conclusion This study provides the first case of molecularly confirmed Cytauxzoon sp. infection in a domestic cat in Germany and describes the clinical picture of the disease in association with FIV infection. These findings suggest that cytauxzoonosis should be considered as a differential diagnosis in cases of anaemia in domestic outdoor cats, particularly in areas where wild felid populations are present.