A single nucleotide polymorphism (SNP) has been previously associated with EHV-1 neurological disease in several countries around the world. This disease is very uncommon in Australia and little information is available about the presence of this SNP in Australian EHV-1 isolates. The ORF30 sequence of 66 Australian EHV-1 isolates was determined and the genotype was compared to the disease manifestation of the case from which the virus was isolated. Of the 66 isolates, 61 were from cases of abortion and 5 were cases associated with equine herpesvirus myeloencephalopathy (EHM). There was no association between pathotype and genotype in these isolates. In total, 64 of the 66 isolates encoded N752, including 4 isolates from EHM cases. The ORF30 sequence was also determined for 14 EHV-4 isolates, including 2 isolates from confirmed EHV-4 abortion cases. All 14 EHV-4 isolates had aspartic acid at the position equivalent to EHV-1 AA752. Aspartic acid was also confirmed in this position for the single isolate of AHV-3 sequenced in this study. The nucleotide sequence of ORF68 was also determined and showed considerable genetic heterogeneity in the EHV-1 isolates, however, this ORF was highly conserved among the 14 EHV-4 isolates sequenced, with only one SNP identified among 7 isolates. These results confirm that the EHV1 ORF30 N752 is unique and that the D752 sequence is most likely to be the true parent strain of this virus. We suggest that the abortigenic form of EHV-1 should be considered to be the more recently emerged mutant.