The Meteor Shower of Smallville was a famous meteor shower of Kryptonite, which fell upon the town of Smallville. In addition to devastating the town, the meteor shower had other lasting effects. First, the new abundance of Kryptonite radiation led to many people becoming mutated or otherwise gaining strange powers and abilities; these people became known as Meteor Freaks. (Smallville Episode 101: Pilot).
Additionally, the Meteor Shower marked the arrival of a baby Superman to the earth. Presumably, the Kryptonite from the destruction of Krypton was caught in the warp field of young Kal-El's spacecraft, thus being dragged along to Earth.
In the comics, there wasn't as blatent a meteor shower in Smallville, however a large amount of Kryptonite was dragged along to Earth by the spacecraft. Some of it did, in fact, land in Smallville.