Individuals with Disabilities Education Act Amendments of 1999 - Amends the Individuals with Disabilities Education Act (IDEA) to revise provisions relating to the placement of children in alternative educational settings under IDEA. Eliminates a 45-day maximum on certain extended (beyond ten-day) alternative placements (currently allowed in cases of a child's carrying weapons or possessing, using, or selling drugs at school or a school function). Allows a school to also place a child with a disability in an alternative educational setting for such an extended period if the child intentionally exhibits violent behavior that has resulted in, or could have resulted in, physical injury to the child or to others while at school or at a school function under the jurisdiction of a State or local agency.

Limits the corrective actions that the Secretary of Education may take against a State that does not provide IDEA services to 18- to 21-year-old prison inmates to a proportionate withholding or reduction in Federal IDEA funds.