Historically, when medical knowledge has not been sufficient, blame always follows. When the Black Death hit Europe in the 1340's, this is exactly what happened. European Jew's, who at this time were doing rather well financially, were the ones who took the rap. Jew's, whose religion promoted cleanliness, were among the least susceptible to Bubonic Plague because they managed to distance themselves from the reservoir of the disease, rats, and its vector, the flea. Of course, the nobles also lived relatively free of risk. So why then, were the Jews blamed? It turns out, the nobles quickly jumped into the blame game, eager to get rid of the Jews to whom they owed money.
As the disease claimed millions of lives, suspected Jews were objected to torture, during which they were interrogated regarding their role in the plague. These Jews, faced with the choice to either admit to their wrongdoing, or suffer continued torture, had a tendency to admit to anything suggested by their interrogators. One documented confession was that of the Jew Agimet of Geneva, who admitted that a Rabbit Peyret assigned him the task of going on a journey to Venice (and various other places affected by the plague) to poison the wells, thus infecting the population. (Remember that Jews usually drank from the wells of separate districts, making this a plausible reality.)
As word of confessions such as this made its way around Europe, things started to look very grim. Jews throughout much of Europe were burned and killed for their undeniable role in the spread of the plague. As documented in Strasbourg, Germany, "On Saturday - that was St. Valentine's Day-they burnt the Jews on a wooden platform in their cemetery. There were about two thousand people of them. Those who wanted to baptize themselves were spared. [Some say that about a thousand accepted baptism.] Many small children were taken out of the fire and baptized against the will of their fathers and mothers. And everything that was owed to the Jews was cancelled, and the Jews had to surrender all pledges and notes that they had taken for debts. The council, however, took the cash that the Jews possessed and divided it among the working-men proportionately. After this, wealth was divided among the artisans some gave their share to the Cathedral or to the Church on the advice of their confessors."
With no knowledge of epidemiology and disease, people struggled to find an answer to the problems of the plague. When the Jews were blamed, they had no way of fighting back, and with all odds against them, Europe gave in to the temptation of blame. Either for money or for a fruitless attempt at atonement, Jews around Europe were killed. Luckily, today this is no longer an issue, and instead of killing each other, we try to find a solution to the problems that we are doing a better job of understanding every year.