That’s another question that brings quite a few visitors. About.com offers The History of Smallpox:
The origin of smallpox is uncertain, but it is believed to have originated in Africa and then spread to India and China thousands of years ago. The first recorded smallpox epidemic was in 1350 BC during the Egyptian-Hittite war. Smallpox reached Europe between the 5th and 7th centuries and was present in major European cities by the 18th century. Epidemics occurred in the North American colonies in the 17th and 18th centuries. At one time smallpox was a significant disease in every country throughout the world except Australia and a few isolated islands.
The thing that pops up first in that search is an article from 1923 which argues that smallpox vaccines were ineffective and that smallpox was caused by poverty and uncleanliness. Poverty and filth obviously have an important role in many forms of disease transmission, but are almost never directly causative.
It’s not that the doctor was unscientific in 1923. The germ theory was still developing, and he had some interesting data. He was wrong though. Vaccines eradicated smallpox in 1977, a year before I was born. Somalia, the site of the last known case, is still filthy and poor, so that’s not what did it.
That’s how science works. We build on our mistakes.