Born and raised in poverty in the Brazilian municipality of Lagoa da Prata, Gilberto joined the youth academy at local club América Mineiro, where he made his senior debut as a centre-back in 1998. After starring the following season, where he helped gain the club promotion into the Campeonato Brasileiro Série A, he joined city rivals Atlético Mineiro. During his time at Atlético, Gilberto transitioned into a defensive midfielder under head coach Carlos Alberto Parreira, and flourished in his new role, gaining a call-up to the Brazilian national team for the 2002 FIFA World Cup, where he featured prominently as his country won the tournament.