Healthy Farms, Foods, and Fuels Act of 2006

Healthy Farms, Foods, and Fuels Act of 2006 - Extends: (1) the conservation reserve program; (2) the wetlands reserve program; (3) the conservation security program; (4) the grassland reserve program; (5) the environmental quality incentives program; (6) the wildlife habitat incentive program; (7) the agricultural management assistance program; and (8) the organic agriculture research and extension initiative.

Establishes: (1) the cooperative conservation partnership initiative; (2) the suburban and community forestry and open space program; (3) an integrated pest management initiative; and (4) a conservation initiative for socially disadvantaged farmers and ranchers.

Revises: (1) the farmland protection program; (2) funding for the healthy forests reserve program; and (3) the national organic certification and transition cost share program.

Makes permanent funding available for: (1) the education grant program for Hispanic-serving institutions; and (2) the fresh fruit and vegetable program.

Revises and extends the biorefinery development program.

Extends: (1) the energy audit and renewable energy development program; (2) the renewable energy systems and energy efficiency improvements program; (3) the Department of Agriculture bioenergy program; (4) biomass research and development; and (5) carbon cycle research.

Extends: (1) the community food project grant program; (2) the farm-to-cafeteria program; (3) WIC farmers' market nutrition program; (4) the senior farmers' market nutrition program; and (5) farmers' market promotion program.