Of 31 needles found in the toddler's body, only one will be left after Monday's surgery, doctors said. A needle in the boy's pubic bone does not cause any danger to his life.
Police have formally accused the boy's stepfather, Roberto Carlos Magalhaes, and his lover of attempted murder for allegedly sticking the needles.
Magalhaes told Globo TV last year he wanted to kill the child to spite his wife, with whom he fought a lot.