Everyone says that people have souls. What happens to the souls of people who have mental retardation, down syndrome, cerebral palsy, autism, traumatic brain ingury? How are these diagnoses explained by religion? In other words, how does religion explain why these things happen to people?

well going into the whole reincarnation idea, maybe the body that the soul was in last time was not such a good person. so the soul has to come back here and pay for wat it has done. it is a punishment and atones for sins. for example, if someone watched things that they should not have watched, then the body that soul goes into next MIGHT come out to be a blind person.
i dont really know too much about this topic from my own research. its just wat i picked up in a few lectures.
the point is that u have to be very careful with wat u use ur body parts for in this world.

but then u can ask, y should a person get punished like this and live such a tough life because of wat a past person who had his soul did. well, really the body is not the person. its just an outside mask. ur not really tsippa, u r ur neshama (soul).

we really dont know the reason y ppl come out like this. Hashem has His own reasons. just know, shekol min hashamayim.

That's how Kaballah explains it. The person with physical deficiencies suffers for the sins of the soul's previous carrier - measure for measure, an eye for an eye. From the human point of view it might appear unfair, but it's not so in the heavenly world.

Actually, a while back there was a series of acticles in the magazine "Druzhba" about this.