Comprehensive Indian Fetal Alcohol Syndrome Prevention and Treatment Act - Amends the Indian Alcohol and Substance Abuse Prevention and Treatment Act to authorize the Secretary of Health and Human Services to make grants to Indian tribes to establish Fetal Alcohol Syndrome (FAS) and Fetal Alcohol Effects (FAE) programs. Authorizes appropriations. Requires that ten percent of the funds appropriated be used for Urban Indian organizations funded under the Indian Health Care Improvement Act.

Requires the Secretary to assist Indian tribes in: (1) the development, printing, and dissemination of education and prevention materials on FAS/FAE; and (2) the development and implementation of culturally sensitive assessment and diagnosis tools for use in tribal communities.

Directs the Secretary to convene a FAS/FAE Task Force to: (1) examine the needs of Indian communities and current Federal resources; and (2) develop an annual plan for the prevention, intervention, treatment, and aftercare for those affected by FAS and FAE in Indian communities.

Requires the Secretary to make grants to tribes and urban Indian organizations for applied research projects proposed to elevate the understanding of methods to prevent, intervene, treat, or provide aftercare for persons affected by FAS or FAE. Authorizes appropriations. Provides that 50 percent of such appropriated funds shall be used for such projects.

Directs the Secretary to report annually to the Congress on the status of FAS/FES in the Indian population, along with recommendations on legislation needed to improve the prevention, intervention, treatment and aftercare of individuals affected by FAS/FAE in Indian communities. Authorizes the Secretary to contract the production of this report to a national organization specifically addressing the FAS/FAE issue. Authorizes appropriations.