Genomic selection programs generate deep pedigrees with whole genome genotyping data, which can also be used for the analysis of genetic defects. Recently, studies highlighted the relevance of novel mutations for human health. The use of non-progeny tested very young sires in genomic selection programs increases the danger of an unnoticed, rapid spread of novel mutations, if no respective precautions are taken. Recently, we identified a novel defect (spinal and vertebral malformation, VSD) and its causal mutation in Holstein cattle. Based on 50K SNP data, in our project 73 offspring of a carrier sire for VSD (41 VSD affected, 31 VSD unaffected) were haplotyped using CRIMAP options, and the paternal haplotype carrying the VSD mutation was identified. To further trace the origin of the haplotype associated with VSD, we subsequently haplotyped 50K SNP genotypes of a total of 55,384 individuals from the German Holstein population including all available relatives of the carrier sire using BEAGLE. Genotypes were provided by VIT Verden, the central database for genomic evaluation in German Holstein cattle. Tracking of haplotypes and haplotype breakpoints through the pedigree excluded the father of the carrier sire as potential source of the mutation and indicated that the mutation was located on the paternally inherited haplotype of the dam. Sequencing of the bovine brachyury gene in the maternal grandsire, the dam and the carrier sire itself revealed that the mutation developed de novo in the dam, because the haplotype of the maternal grandsire that was transmitted to the dam contained the wild type allele, whereas the respective haplotype in the dam showed the mutated allele. Additional genotyping of 94 offspring of the maternal grandsire revealed that none of those offspring showed the mutated allele. In conclusion, population-wide SNP genotyping and haplotype tracking enabled exclusion of a major Holstein blood line as source for VSD and confirmed the origin of the defect. Due to the recent de novo mutation and the confirmed knowledge about the founder, the defect can easily be eradicated from the Holstein population before any further outspread.