Horse breeders rely heavily on the accurate identification of individual ancestry through pedigrees. Errors in such pedigrees may inaccurately assign horses to false lineages or breed memberships, and can result in inaccurate estimates of inbreeding. Discrepancies in pedigree records can lead horse owners into making misguided purchasing and breeding decisions. Genome-wide SNP data provide a robust and precisely quantitative tool to resolve many lineage assignments and provide genomic measures of inbreeding values. The aim of this project was to pilot a comparison between pedigree and genomic relatedness measures. Here, we describe a herd of 36 pedigreed Egyptian Arabian horses genotyped using the Equine SNP70 (Geneseek, Inc.) Genomic inbreeding values and pair-wise relatedness between horses within the herd were estimated from the genotypic data. Pedigree derived inbreeding values were significantly correlated with the genomic inbreeding values across the population (r = 0.44, P = 0.007), although within an individual the 2 values could differ substantially. Genomic inbreeding values were also positively correlated with the year of birth (r = 0.29, P = 0.086), demonstrating a trend in inbreeding over the years. A multi-dimensional scaling analysis (MDS), a phylogenic analysis and a clustering analysis were preformed to compute the relationships between the horses and the results were compared with the pedigree information. These same analyses were also conducted for the herd among US, Polish, and Egyptian Arabian horses to examine their Arabian ancestry. The within herd analysis was successful in recapturing much of first-degree relationships, although more distant relationships were not entirly reconstructed. The herds’ Egyptian lineage was successfully assigned among Arabian horse sub-groups. It can be concluded that genome-wide genotypes are good alternatives to compute inbreeding and verify the integrity of pedigrees in horses in cases where records are unavailable or in doubt. Although costly, application of this tool in a breeding program can enable informed mating decisions and assess inbreeding in lines of horse already at risk of loosing genomic diversity.