Equine herpesvirus type 1 (EHV-1) is a worldwide spread pathogen of horses. It can cause abortion, respiratory and neurological disease and consequentially significant economic losses in equine industries. During 2009, two outbreaks of EHV-1 were confirmed in two stud farms in Eastern Croatia. The first outbreak occurred in February following the import of 12 horses from USA, serologically negative to EHV-1 before transport. Four mares aborted in the late stage of pregnancy and one perinatal death was recorded. Other six mares showed clinical signs of myeloencephalopathy with fatal end in four. One month later, the second EHV-1 outbreak was confirmed in stud farm about 100 km further with 17 abortions, three perinatal deaths and one mild neurological case. Epidemiological data showed that the disease was probably introduced in the first stud farm during international transport. The second outbreak started with the introduction of clinically healthy stallion from the first stud farm. Molecular characterisation and phylogenetic analysis confirmed that, despite different clinical signs, the identical virus caused both outbreaks. Both horse populations were free from EHV-1 infection before the outbreak and had not been vaccinated. Significant difference in clinical signs could be explained by different breed-related risk factors.