Anaplasma phagocytophilum, transmitted by Ixodes ticks, is an intracellular pathogen of zoonotic interest. Regarding animals of veterinary importance, infection by this agent has been linked mainly to high fever, neutropenia, reduced milk production, but hemorrhagic diathesis, abortion and impaired spermatogenesis have also sporadically been reported. In Greece, A. phagocytophilum has been detected in dogs, ticks and humans, while so far only A. ovis had been detected in farm animals. Following the occurrence of multiple abortions in two goat farms in Northern Greece, samples were collected from aborted animals. Stomach contents and placental tissue from aborted animals tested positive for A. phagocytophilum by molecular assays and negative for other infectious and parasitic agents. Treatment with oxytetracycline LA stopped the abortions. In tick risk areas clinicians should consider A. phagocytophilum as a cause of abortion in goats.