The short answer
Yes, mutts—on average—are healthier than purebred dogs, although this does not mean that individual mutts always have fewer health problems than individual purebred dogs.
The long answer
To fully answer this question we first need to understand how purebred dogs came about.
Over many generations, certain dogs with specific traits—like coloring, size, and behavior—were selectively bred together.
This led to groups of related dogs with shared physical characteristics (i.e., phenotypes) and genetic characteristics (i.e., genotypes).
These groups of closely related dogs are called "breeds."
Selective breeding can create extreme traits
Selective breeding, also called "artificial selection," can be a powerful process.
Over thousands of generations, selective breeding has shaped the domestic dog into an extremely diverse species.
In fact, no land mammal matches the domestic dog when it comes to the possible spectrum of diversity between individuals.
What other species, as an adult, can weigh two pounds, like a Teacup Chihuahua, or two hundred pounds, like an English Mastiff?
That’s a 100-fold difference!
Selective breeding can lead to health problems
Imagine if the same were true for humans.
You might see giants who weighed half a ton walking around banging their foreheads on street lights.
As fun (and exaggerated) as that may be, we should think twice before we convince bigger and bigger people to get hitched and have kids (never mind the moral issues).
"Bad" genes may be passed along with "good" genes
Breeding for desirable traits can also bring out some undesirable characteristics, as other traits can get carried along for the genetic ride.
Literally.
A "good gene" that is being selected via breeding could be physically near a "bad gene" on a chromosome, increasing the chances that offspring inherit both good and bad traits.
That’s why most breeds are infamous for at least one genetically based health issue.
For example, Dobermans are prone to enlarged hearts, Shar Peis often have skin ailments, and Rhodesian Ridgebacks are known for a particularly awful condition called dermoid sinus, in which dogs are born with tunnels through their skin, sometimes all the way to the spinal cord.
Yes, that is a problem.
Extreme traits aren't always compatible with life
Other health problems in purebred dogs may not be due to a tagalong gene, but to what I would call "taking it too far."
The Bulldog is a good example of this.
Here is a drawing from 1889 of an English Bulldog.
And here is a photo of Star, English Bulldog and winner of the 2022 AKC National Championship.
Notice anything different?
I see two major differences.
First, Star is much stockier than the Bulldog from 100+ years ago. This is partly due to breeding for shorter limbs—sort of like breeding for dwarfism—which increases risk of joint problems.
Second, and maybe more importantly, despite being a supposed best in breed, Star has almost no snout. Sure, dogs with smooshed faces are cute, but those short/nonexistent snouts lead to poor airflow, chronic hypoxia (low oxygen to the brain and other tissues), snoring, challenges with physical activity, and even respiratory failure (yes...death...which is a problem).
Why mutts are usually healthier
Mutts tend to be healthier, on average, because they come from a more diverse gene pool.
This means it is less likely for specific genes to be inherited for reasons other than survival, which makes it is less likely that "bad genes" get passed down.
Incidentally, this is why you shouldn’t "kiss" your cousin (as though you needed reminding).
Bonus fact: Charles Darwin was a cousin-kisser
Charles Darwin married his first cousin and should have known better.
He even expressed concern that this inbreeding might lead to health problems in their children.
He was right to worry.
Three of his ten offspring died in childhood. Of the six who lived long enough to have long-term marriages, only three had kids of their own, hinting at issues with infertility.
You've been warned!
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