Breeding and health issues

Besides infectious diseases, viral diseases like rabies, bacterial, fungal and other diseases there're also genetic diseases

Genetic conditions are a problem in some dogs, particularly purebreeds. For this reason many of the national kennel clubs require that dogs with certain genetic illnesses or who are deemed to be carriers cannot be registered. Some of the most common conditions include hip dysplasia, seen in large breed dogs, von Willebrand disease, a disease that affects platelets that is inherited in Doberman Pinschers, entropion, a curling in of the eyelid seen in Shar Peis and many other breeds, progressive retinal atrophy, inherited in many breeds, deafness, and epilepsy, known to be inherited in Belgian Shepherd Dogs, German Shepherd Dogs, Cocker Spaniels, and St. Bernards.
Subaortic stenosis, or SAS, is a genetic ailment that causes a narrowing of the passage of blood between the heart and the aorta. This leads to heart problems and sometimes sudden death. It affects larger breeds such as the Newfoundland Dog and the Golden Retriever. In some dogs, such as collies, the blue merle or harlequin coloring is actually the heterozygote of a partially recessive gene preventing proper development of the nervous system; therefore, if two such dogs are mated, on the average one quarter of the puppies will have severe genetic defects in their nervous systems and sensory organs ranging from deafness to fatal flaws.
Pedigree Dogs Exposed was a BBC One investigative documentary, produced by Jemima Harrison, which looked into health and welfare issues facing pedigree dogs in the United Kingdom.

The Kennel Club (KC), the governing body of pedigree dogs in the UK that runs the prestigious dog conformation show Crufts, was criticized for allowing breed standards, judging standards and breeding practices to compromise the health of pedigree dogs.
Deliberate inbreeding, including mother-to-son, father-to-daughter and brother-to-sister matings was said to result in serious genetic disease being perpetuated in many breeds. A 2006 report by Companion Animal Welfare Council called for major changes, stating that "inbreeding needs to be controlled" and that "animals with genetic defects should be barred from breed shows." Irving rejected the claims in the report, saying that it was based on emotion rather than science.
A 2004 paper authored by the Kennel Club's own geneticist Jeff Sampson mentioned that "Unfortunately, the restrictive breeding patterns that have been developed as part and parcel of the purebred dog scene have not been without collateral damage to all breeds..." and that "increasingly, inherited diseases are imposing a serious disease burden on many, if not all, breeds of dogs." Yet when interviewed for the programme, Sampson claimed that "the vast majority of dogs we register [...] will live long, happy, and healthy lives." A study by Imperial College, London, showed that the 10,000 pugs in the UK are so inbred that their gene pool is the equivalent of only 50 individuals.
On 7 October 2008 the Kennel Club announced that it is rolling out new health plans. Breed standards for every breed are under review and show judges will be required to take health into judging considerations. It has also requested regulatory powers from the Government, which would allow the club to take actions against breeders who do not comply with health standards. Some breed clubs have condemned the Kennel Club for overreacting. The bulldog breed council has rejected the new Bulldog standard, saying that they are "at a loss to understand in what way the health and general welfare of the breed could be improved by the proposed changes".
On 12 January, the Kennel Club released the revised breed standards, which will "not include anything that could in any way be interpreted as encouraging features that might prevent a dog from breathing, walking and seeing freely." "This will help to prevent the practice of exaggeration, where features that are perceived to be desirable, such as a short muzzle or loose skin, are made more prominent by breeders, and which can have detrimental effects on a dog's health." Rules to ban close inbreeding (parent/child and sibling/sibling) would take effect 1 March 2009. Show rules have been changed to state "more clearly than ever" that judges should only "reward those dogs that are healthy representatives of their breed." Judges will also have the authority to eject unhealthy dogs from competitions. A Club spokesman said that the changes would take "several generations, to have an effect."
Pedigree Dogs Exposed producer Jemima Harrison calls the change "long overdue". RSPCA chief vet Evans welcomed the ban on close inbreeding but said that the breed standard changes were not "radical enough to really make a difference." He also expressed concern about how standards would be interpreted in the show ring. While some breeders have shown their support for the new standards, others are upset with the new standards and have threatened legal actions against the Kennel Club. The Chairman of the British Bulldog Breed Council said of the new Bulldog standard: "What you'll get is a completely different dog, not a British bulldog. There is no jowl, no upturn of the nose and the legs will no longer be wide in front and narrow behind."

Text from Wikipedia
Additional health issues concerning Maltese you'll find here!
One article you may be interested in is Encephalitis in Maltese (GME).