Cavalier King Charles Spaniels are among the affected breeds
The RSPCA says it is to withdraw from Crufts dog show amid concerns about the health of pedigree animals.
It is to scrap its regular welfare stand at the contest next March.
The charity says "morally unjustifiable" breeding practices lead to disability, deformity and disease among show dogs.
The Kennel Club, which runs Crufts, has insisted the vast majority of dogs are healthy but it recognised there were some problems with certain breeds.
It says it is working hard to improve the health of dogs.
RSPCA chief veterinary adviser Mark Evans has called for a shift in emphasis away from the looks of dogs and towards their health, welfare and temperament.
He said judging criteria used by shows such as Crufts encouraged inbreeding and the rearing of deformed dogs, as demonstrated by BBC documentary Pedigree Dogs Exposed.
"There is compelling scientific evidence that the health and welfare of hundreds of thousands of pedigree dogs is seriously compromised as a result," said Mr Evans.
"From a dog health and welfare perspective, such shows are fundamentally flawed and do our much-loved pedigree dogs no favours.
"Intentionally breeding deformed and disabled animals is morally unjustifiable and has to stop."
Among the cases highlighted in last month's documentary was a prize-winning Cavalier King Charles spaniel with syringomyelia, which occurs when a dog's skull is too small for its brain.
The programme also featured boxers suffering from epilepsy, pugs with breathing problems and bulldogs which were unable to mate or give birth unassisted.
RSPCA vets wants to see the development of health-focused breeding strategies for individual breeds, including steps to increase their genetic diversity.
In the past the charity, which is also pulling out of the Discover Dogs show in November, has staffed a stand at Crufts to promote general animal welfare.
Kennel Club spokeswoman Caroline Kisko said its research showed 90% of pedigree dogs would not suffer health problems that would have a detrimental effect on their quality of life.
She said: "The fact that the RSPCA continues to make such unhelpful statements with regard to the health of pedigree dogs is extremely regrettable."
The Kennel Club was dedicated to improving the health and welfare of dogs through responsible breeding, while shows like Crufts played a valuable educational role in this, she said.
Mrs Kisko said the club's charitable trust invested heavily in developing health screening for dogs and had recently donated £48,000 to the RSPCA.
Show judges rewarded dogs that meet a particular breed standard, which is the blueprint for a healthy dog, she added.