Before playing in the NHL, Michálek played 2 seasons with HC České Budějovice of the Czech Extraliga. He was drafted by the San Jose Sharks with the 6th overall pick in the 2003 NHL daft. He played 4 seasons with the Sharks and was then on September 12, 2009, he was traded to the Senators along with Jonathan Cheechoo and a second round pick for Dany Heatley and a fifth round draft pick in 2010.