Even though most people will say he died of natural causes, let's put some facts in perspective and then give it another ponder.
Pol Pot was being held by his former commrades in what was left of the Khmer Rouge. He had turned on them, and they on him. These were his partners in crime during the 1975-79 genocide.
Shortly after they announced they had captured Pol Pot, then U.S. President Bill Clinton made a public announcement that, along with the Thai government, the U.S. would send in troops to apprehend him and bring him to justice. Once in custody, he would most likely tell all, hoping to gain leniency. If you were one of the former war criminals holding him, wouldn't you be inclined to do something to stop him from implicating you?
Not so surprisingly, just days after Clinton's announcement, it was announced that Pol Pot had suddenly died, from a heart attack, as it was explained. He was creamated the next day before anyone could examine the body.
More likely, Bill Clinton's announcement signed Pol Pot's death warrent. It was either an egregious order of extra-judicial execution which precluded testimony that would have brought the whole Khmer Rouge organization to justice, or it was one of the biggest diplomatic blunders in American history.