Equine herpesvirus 1 (EHV-1) causes considerable economic loss to the equine industry and is spread among susceptible animals during the cycles of latency and reactivation, causing rhinopneumonitis, abortion, and neurological disease. Nucleotide polymorphisms within ORF30 and ORF68 sequences of the viral genome are associated with strain neuropathogenicity and geographical origin. A total of 142 tissue and nasal swab samples from apparently healthy unvaccinated horses were examined to ascertain EHV-1 distribution, diversity, and clinical significance considering the results of virus isolation, sequence analysis, and anamnestic data. The ORF30 and ORF68 molecular study of these circulating strains and archival isolates from abortion storms aimed to contribute to the perception of strain pathogenicity and origin. EHV-1 was detected by PCR and virus isolation in 81 and 45.1% of the analyzed samples, respectively, and 82.1% of the representative samples were neuropathogenic strains. The ORF68-based grouping was restricted by the pronounced polymorphism of Balkan EHV-1 strains, and only two isolates were assigned to group 4. The cases of abortion were caused by neuropathogenic strains that also circulate within the horse population with no documented outbreaks of disease. It was evident that strain virulence is not solely accountable for the development of clinical symptoms in affected animals. Neural tissue is significant for virus latency and reactivation, considering the number of EHV-1 isolates from apparently healthy stressed horses. Special care must be taken when accommodating together immunologically naive and latently infected horses since asymptomatic carriers silently shed EHV-1.