School Safety Act of 1999 - Amends the Individuals with Disabilities Education Act (IDEA) to authorize school personnel to order a change in the placement of a child with a disability to an appropriate interim alternative educational setting for the same amount of time that a child without a disability would be subject to discipline, but for not more than 45 days, except with respect to specified weapons violations.

Authorizes school personnel to discipline (including expel or suspend), in the same manner in which such personnel may discipline a child without a disability, a child with a disability who: (1) carries or possesses a weapon to or at a school, on school premises, or to or at a school function under the jurisdiction of a State or local educational agency (LEA); or (2) threatens to do so, which includes behavior in which a child verbally threatens to kill another person.

Declares that a child expelled or suspended shall not be entitled to continued educational services, including a free appropriate public education, during the term of such expulsion or suspension, if the State does not require a child without a disability to receive educational services after being expelled or suspended. Authorizes the LEA, even if State law does not require it to do so, to choose to continue to provide educational services, at any level of services and at a site it chooses.

Amends the Gun-Free Schools Act of 1994 to subject certain provisions to IDEA requirements added by this Act for school expulsion or suspension, because of a weapons violation, of a child with a disability.