Assisted Suicide Prevention Act of 2006 - Amends the Controlled Substances Act to prohibit medical practitioners from using a controlled substance for the purpose of assisting suicide or causing the death of any person. Provides that dispensing, distributing, or administering a controlled substance to alleviate pain or discomfort in the usual course of professional practice consistent with public health and safety is a legitimate medical purpose, even if the use of such substance may increase the risk of death.