Lee Cook began his career at non-league club Aylsebury United. Once he had worked his way through the ranks from the youth team he made 19 appearances and scored 2 goals. In 1999 Lee moved to Watford FC after an impressive trial period. In the four years he spent at Watford he played in the FA Premiership and the Championship, he made 64 appearances, scoring 7 goals. Cook spent 2 months at York City FC on loan in 2002 and made 7 appearances with them and scored once.