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A fictitious (not fantasty) story is set in a third-world country sometime during the 70s or 80s. The country operates similarly to any semi-developed country in central or south America. The countryside is barely developed, with maybe some token schooling. In the cities there is some technology, like airplanes and cars. The country has an armed police force (or soldiers), again present primarily in the cities. The vast majority of the citizens live in poverty.

It possesses one unique feature: they capture, persecute, and possibly kill autistic children. They will use force to take the children away from their families and will even prevent efforts to send an autistic child out of the country.

What would cause a culture to persecute people with autism?

A fictitious (not fantasty) story is set in a third-world country sometime during the 70s or 80s. The country operates similarly to any semi-developed country in central or south America. The countryside is barely developed, with maybe some token schooling. In the cities there is some technology, like airplanes and cars. The country has an armed police force (or soldiers), again present primarily in the cities. The vast majority of the citizens live in poverty.

It possesses one unique feature: they capture, persecute, and possibly kill autistic children.

Superstition.

Autistic children can -- in all honesty -- behave Very, Very Strangely. If you're highly religious, then an autistic child can look demonically possessed.

Some people want to exorcise the demons -- "the power of Christ compels you!" -- but others -- and they just happen to be the ones in power -- want to drive a stake through their hearts and bury them in pits in unsanctified ground.

For the same reason that autistic people often have trouble in most societies today: The tendency toward literal observation and very direct speech. This can cause all sorts of trouble (think about telling your boss exactly what you think of her management style), and just "refrain from commenting honestly" can be difficult enough, much less the polite lies that are the typical social lubricant.

Combine this emperor-has-no-clothes straightforwardness with a society where political correctness is Serious Business, such as the Soviet Union (where people were afraid to be the first to stop clapping for political speeches), and you have a situation where being autistic (or inconveniently honest in general) will get you disappeared.

NOTE: My notes are for the United States, though there will be many similarities with other industrialized countries. And non-industrialized countries.

This is not unique.

Capturing and persecuting disabled children (in other words, putting them in institutions) was a very common response to "difference" in most of the 20th century and also some times before.

I know people who were institutionalized (with the approval of their families) for having Down Syndrome or juvenile arthritis (which doesn't affect intellect, just walking and using your arms). Even children with something as simple as club foot ended up in institutions.

Kids who needed physical adaptations to their environment (places to roll their wheelchair...or the wheelchair in the first place) were institutionalized when they were too big to carry around. Changing the location of the kid was easier than changing the infrastructure.

Mental health issues also were something that frequently pegged people as "unfit" for society. This included women who spoke out against sexism, people of color who were too "uppity," people suffering from trauma (especially things one didn't talk about, like being raped), and people with actual mental illness.

Historically, there were not a lot of people with autism in institutions. Simply because autism wasn't very common. Now it's extremely common (plenty of studies show that only a part of it is due to changes in diagnostic criteria and the increase in diagnosis overall). But if we were still a society with large amounts of institutionalization directly due to disability, the institutions would be filled with autistic children and adults too.

So if your fictitious society targets autistic children, it may simply be because autism is perhaps the most common condition in children with disabilities that aren't overly physical (blindness, losing a limb, etc).

We still have group homes and the like but they are not institutions and they are not for small children. Those kids who can't be with their families mostly go to foster care. But, guess what? We still have capture and persecution of people with disabilities in the US. It's called prison. Huge percentages of modern day prisoners are people with mental illness (often masked by self-medication aka drug abuse) or people who don't "fit in" in some manner or people with other kinds of disability.

With American-style prisons for profit, there's an incentive to increase the prison population. So, if you're part of a marginalized community, it doesn't take much to get sentenced. Then you're put to work. You get paid almost nothing while the prisons take payment from the companies who benefit from the cheap labor.

I'm talking about real life here. I'm not making this stuff up.

So if your world has a lot of people with autism and a lot of oppression of people who are different, then people with autism will be targeted. The only thing you have to do differently from real life is the fact that autism was not common in the 70's and 80's and is not common in 3rd world countries.

In WWII concentration camps targeted "problem" DNA, things that "ruined" the human race like genetically passed defects, homosexuality, and (of highest priority) the Jewish race.

As awful as that is, it's a real event, and it only happened ~80 years ago. Your story could follow a similar thing, where the intention could seem noble to some (who have 0% compassion or humanity) to "purify" the country of autism.

Eugenics + Poverty

If you feel like hating humanity you can look up the practise of forced sterilization, which was quite widespread even 40 years ago. And you still see genocides in 3rd world countries of undesirables, it is not a far stretch to connect autism with undesirables.
All you need is a tiny bit of propaganda in a paranoid or stressed society and they would have no problem doing what you describe, real countries have done far worse.

In 1933he Nazi passed the ‘Law for the Prevention of Hereditarily Diseased Offspring’, allowing for the forced sterilisation of those regarded as "unfit". Only a few years later his included panels for deciding which disabled people should be "mercy killed" instead of just being sterilized. They kept it hushed up enough most families though the people were just being put in special care facilities, later they would be told they had died of some common disease. Most of the techniques they applied to later concentration camps actually started as techniques for "solving" the disabled problem.

If poverty is as common as you say people in your fictional country will likely welcome such measures for the burden they remove. Also keep in mind shame can easily keep people from checking on institutionalized family members so you may not even see much checking to begin with, so the lies only need to be paper.