Who makes shinichi small in detective Conan?

Shinichi Kudo is shrunk to the size of a child by the Black Organization.

Specifically, he is given a powerful, experimental drug called APTX 4869 by a member of the Black Organization named Gin.

Gin tricked Shinichi into taking the drug while investigating the organization's activities. The drug was intended to be a lethal poison, but it backfired, causing Shinichi to shrink instead.