Sheep infected with Anaplasma phagocytophilum, the causative agent of tick-borne fever (TBF), develop humoral immune responses 7–14 days after infection. Those individuals that survive acute TBF develop persistent infection, which may last for several months or even for life. The persistence of infection and recurrent bacteraemia is thought to be due to p44-mediated antigenic variation. The present study mapped linear B-cell epitopes within the hypervariable region (HVR) of the surface membrane protein P44 and investigated whether the development of antibodies against B cell epitopes within the HVR was preceded by the expression of p44 variants. Serum samples obtained from five sheep infected with the Old Sourhope strain of A. phagocytophilum (AP-OS) were used to detect antibody reactivity against 20-mer overlapping synthetic peptides spanning the HVR of two p44 variants which were expressed during primary bacteraemia and 3 variants expressed during secondary bacteraemia. The results showed that all five p44 variants of AP-OS have dominant B-cell epitopes residing mainly in the 3rd and 7th of the 10–11 peptides mapping each HVR. Antibody reactivity against peptides of the HVR of all the variants was characterised by a gradual rise, reaching peak levels in samples obtained 24 days post-inoculation (dpi) followed by a gradual decline. Anamnestic responses to whole cell antigens and to some of the dominant antigenic epitopes were detected in some of the animals, which were monitored for 52 weeks.