The Havanese breed seems to suffer from a wide variety of health problems, though none of these health problems seems to appear with a high frequency. This is most likely due to the fact that Havanese breeders and enthusiasts have dedicated a great amount of time, effort and research into keeping the gene pool healthy and minimizing the risk of disease development. Indeed, the breed is thought to be relatively healthy and the average lifespan for one of these dogs can be anywhere from 12 to 15 years of age. Heath problems do pop up in the breed, though, some more often than others and some more serious than others. One of the health problems seen occasionally in the Havanese is the liver shunt.

Technically, it's called a portosystemic liver shunt and it is a problem found in many small dogs and toy breeds. These shunts are actually common in mammals when they are still inside the uterus; because the maternal placenta delivers oxygen and nutrients to the developing fetus, fetal circulation is a bit different than post-natal circulation. The liver has the function of filtering, cleaning and detoxifying blood; because fetal blood comes from the mother, her liver has already detoxified the blood and so the blood does not have to pass through the fetus's liver. Shortly before birth, the shunt is supposed to shut down, so that the newborn baby's liver can start taking over the function of blood filtration.

In some animals, the shunt does not close down and blood continues to bypass the liver and enter the main bloodstream without being filtered; this is very harmful as toxins could be released into the bloodstream and damage tissues and major organs. Two general types of shunts exist; the intrahepatic shunt is a blood vessel that is found within the liver, while the extrahepatic shunt is outside the liver. Intrahepatic shunts are usually found in larger dog breeds and they are more difficult to resolve with surgery; extrahepatic shunts, on the other hand, are the ones usually found in small breeds, like the Havanese, and have a better prognosis following surgery.

Since the condition is congenital, signs and symptoms can appear before one year of age. Dogs with this condition are usually small and thin, they may suffer seizures (due to the buildup of toxins), vomiting, depression, compulsive pacing, circling, disorientation, aimless walking and some degree of blindness, which could be temporary. As soon as these signs are noted, the dog should be taken in for a complete battery of blood tests and chemical screens. An ultrasonography, portovenography and a radiograph are also useful. For Havanese, surgery is usually successful, though the dog's lifestyle must also be changed to ensure long term maintenance; the dog must either be put on a low-protein diet or must not have any protein at all. Though the disease is rarely fatal, most dogs will have no energy, especially after protein restrictions.