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Dobrava (DOBV) and Puumala (PUUV) viruses are endemic throughout the Balkans and cause haemorrhagic fever with renal syndrome (HFRS). The aim of this study was to assess the impact of two different hantaviruses on renal function in HFRS patients during the acute stage of illness. We also aimed to assess the DOBV and PUUV distribution between symptomatic HFRS patients and asymptomatic hantavirus antibody-positive subjects. The study included 264 symptomatic HFRS patients and 63 asymptomatic hantavirus antibody-positive healthy subjects. In our study, 131 (49.6%) HFRS patients were regarded as PUUV- and 69 (26.1%) as DOBV-infected patients, while in 64 (24.2%) of HFRS patients that showed all clinical and biochemical signs of HFRS, the causal hantavirus could not be determined with commercially available tests. DOBV-infected patients were associated with more requirements for haemodialysis treatment, lower diuresis and higher serum creatinine and urea values compared to PUUV-infected patients. PUUV was significantly predominant in asymptomatic hantavirus antibody-positive subjects (69.8%) compared to HFRS patients. DOBV was present in 17.5% of asymptomatic subjects and, interestingly, the preferential hantavirus serotype could not be determined in 12.7% of the asymptomatic antibody-positive subjects.