Lavender foal syndrome (LFS) is a fatal hereditary condition that is inherited in an autosomal recessive pattern. This detrimental mutation is more common in Arabian foals of Egyptian origin than foals from other bloodlines. Heterozygous horses are carriers of the LFS trait and appear normal, while recessive homozygous foals died shortly after birth due to serious complications. In Egypt, in 2014, an Egyptian foal died after manifestations of neurological signs and abnormal coat colour as LFS signs. Therefore, it is important to identify LFS carriers in the population of Arabian horses in Egypt and to encourage improvement of the Arabian horse industry in Egypt by constructing a breeding system based on genetic background in order to avoid mating between carriers and reduce financial losses from deaths of affected foals. Objectives: To establish a PCR-based test for detecting the MYO5A gene mutation causing LFS in the registered Arabian horse population in Egypt prior to breeding. Study design: Cross sectional survey (n = 170) plus targeted sampling (n = 30). Methods: A total of 200 samples were collected from an Arabian farm in Egypt and some of them were traced for LFS based on the farm records. The LFS genotypes were identified using the PCR-RFLP technique, fragment analysis followed by sequence analysis. Results: The overall mutated allele and genotype frequencies (N/L) were 0.08 and 16%, respectively. Conclusion: The observed frequency of heterozygotes suggests foals affected with LFS will be produced among Arabian horses in Egypt. Therefore, screening of the entire population for this mutation should be undertaken in the breeding program.