The incidence of perinatal mortality of Arabian horses in Croatia is in accordance with the high frequency of lethal and sublethal mutations in Arabian horses in other countries. The objective of this study was to investigate the frequency of recessive genes causing lavender foal syndrome (LFS) in three Croatian breeds of Arabian horse and to compare these findings with the literature reports. Pedigree and molecular analyses indicated the existence of three distinct breeds of Arabian horses (Traditional Arabian, Shagya Arab, and Pure Arabian horse) in Croatia. Molecular analyses were performed on 100 blood samples (n = 100) of Arabian horses by analyzing isolated and quality-tested genomic DNA. Polymerase chain reaction-restriction fragment length polymorphism analysis of the MYO5A gene was performed for LFS determination. The proportion of heterozygous carriers and the frequency of the LFS allele were lower in Arabian horse breeds in Croatia than in other reports. The LFS allele was found exclusively in the Pure Arabian breed, supporting the findings of other studies on Egyptian Arabian horses. The results are consistent with the interbreeding of Pure Arabian horses in Croatia with Egyptian Arabian horses. The Traditional Arabian and Shagya Arab breeds showed a lower frequency of the LFS allele. Based on these results, screening of the entire population of Arabian horses in Croatia for mutations responsible for multiple inherited genetic disorders should be included in breeding programs.