As mentioned before, Beagles are relatively healthy dogs, though they do suffer from a few genetic problems, some of which can be serious. One of these serious problems is incorrectly labeled "dwarfism", though the term is widely used. The medical term for the condition is osteochondrodysplasia, chondrodysplasia or chondrodystrophy and it is actually a series of problems involving the cartilage and bones, most often of the feet and legs, though the spine may become involved as well. Indeed, the term "osteo" means bone, the term "chondro" refers to cartilage and the term "dysplasia" involves abnormal development. The disorder is genetic in nature and there is no cure.

Cartilage is actually the precursor to bone in mammal skeletons, with the fetal framework being entirely made out of cartilage until it is replaced by bone. In some cases, problems occur in this replacement process and this may lead to deformities in the size or shape of bones. The range of disorders classified under chondrodystrophy cause the limbs of the dog to be disproportionately short; this result is what has led individuals to call the disease "skeletal dwarfism." The condition has also occasionally been called "the Funnies", though there isn't much to laugh about.

Since it caused by an autosomal recessive gene, two healthy looking parents may have one or more affected puppies. Puppies are most often born with the disorder, though signs or symptoms may not be visible until several weeks of age; X-rays must be done to ascertain the condition of the puppies with certainty. As the disease progresses, the limbs of the dog become abnormal in shape and in length, often leading eventually to the dog becoming painfully deformed and crippled. The carpal and radius bones of the front legs are the parts of the canine body most commonly involved and affects of the disease range in severity; some afflicted dogs are almost normal in appearance, simply displaying a short stature (with no clinical issues), while others are severely crippled due to extensive deformations such as bowed limbs, angled limbs, loose limbs, joints that are enlarged and deformed, and lameness.

Dogs suffering from this condition may experience a range of other problems, including serious arthritis and joint pain, deafness, skull deformities and shortened life span. While the limb bones are most often affected, chondrodystrophy can also have an effect on the vertebrae of the spine, causing a shortened body and painful disc disorders. Degenerative disc disease is one of the vertebral disorders associated with chondrodystrophy. Unfortunately, as mentioned, there is no cure for this disease. In cases of mild to moderate chondrodysplasia, joint pain is treated with anti-inflammatory drugs and pain killers, while a surgery may be performed to temporarily correct a painful deformity. In severe cases, experts and owners have painfully agreed that euthanasia is most likely the most humane option, as the dog is so crippled that movement without excruciating pain is impossible.