During the period 2000-2003, patients hospitalized for suspected tick-borne encephalitis in the Czech Republic were screened for possible A. phagocytophilum co-infection. Blood samples taken at admission were tested for the presence of A. phagocytophilum DNA by nested PCR using a modified target sequence as an internal control, and sera were tested for the presence of antibodies by indirect immunofluorescence and western blotting methods using cell-culture-derived antigens. To verify the assay specificity, a set of 45 sera of Patagonian residents served as a non-tick-exposed control group, and a set of 14 B. henselae-positive sera was used to check cross-reactivity. Of 809 patients hospitalized, 80 (9.9%) showed IgG antibodies reactive to A. phagocytophilum at > or =80 (reciprocal dilution factor) and 50 (6.2%) at > or =160; two (0.2%) patients showed elevated IgM titers of 40. No full blood obtained from 162 patients tested positive in PCR when false negativity was excluded. During hospitalization, the diagnosis of tick-borne encephalitis was confirmed in 536 patients, 57 (10.6%) of whom had anti-A. phagocytophilum IgG antibodies reactive at > or =80 and 41 (7.6%) at > or =160, which did not differ significantly from the whole set (P = 0.66/0.30), the maximum IgG titer registered was 5120, and no IgM titer reached the 40 cut-off. Available paired sera from 189 tick-borne encephalitis patients showed no significant shifts, but one case of slight seroconversion (IgG shift from < 80 to 320) was detected in one of the non-tick-borne encephalitis patients. The sex of the patient showed no significance for the prevalence of A. phagocytophilum antibodies; however, the seropositive patients were older on average than those who were seronegative (43.5 +/- 15.9 vs. 37.9 +/- 18.3 years, P = 0.05). Clinical manifestation of the disease did not differ noticeably between patients with and without A. phagocytophilumreactive antibodies, except for fever duration, which was significantly longer in patients with titers > or =1280. Overall, A. phagocytophilum co-infection did not seem to be a frequent and/or significant complication of tick-borne encephalitis acquired in the Czech Republic.