Alopecia X is an inherited disease in Pomeranians and other breeds with plush undercoat. It leads to hair-loss and sometimes also to a darkening of the underlying skin. Male dogs are much more frequently affected than female dogs, which has led to speculations that a hormonal imbalance might be involved in this disease. However, up to now the cause of alopecia X remains unknown. As the underlying problem has not yet been discovered, we employed a purely genetic approach to localize the mutation in the dog genome. Using SNP chip technology and a so-called genome-wide association study, we were able to show that the mutation causing alopecia X resides on a small segment of chromosome 15. This result is an important advance as there are only ~10 genes in this segment. This means that the other ~20’000 genes in the dog genome are not responsible for alopecia X and need not be further investigated. Unfortunately none of the genes in the associated interval on chromosome 15 has a known involvement in hair growth. Therefore, we will next need to perform a very labor-intensive investigation of all variants in this region to be able to identify the causative mutation for alopecia X.