Twelve confirmed cases of equine granulocytic anaplasmosis (EGA) and five additional suspected cases, showing a compatible clinical history and specific IgG titres of 1280 or above, were recorded in the Czech Republic during the period 2002 to 2008. The diagnosis was based on clinical signs, the detection of Anaplasma phagocytophilum morulae in neutrophils in blood smears, serology and molecular methods. Pyrexia (39.8 to 41.3°C), depression, partial or total anorexia, limb oedema and icterus were the most frequently observed clinical abnormalities. Haematological examination revealed thrombocytopenia in all the horses, and mild anaemia and leucopenia in five of them. Several horses showed high titres of specific antibodies immediately after onset of the disease, suggesting that they had previously been exposed to A phagocytophilum. Genotyping of the A phagocytophilum strains distinguished two genetic variants, with divergence in the sequence of the ank gene of the bacterium, circulating in the Czech Republic.