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PFLAG (Parents, Family and Friends of Lesbians and Gays)
202-467-8180
www.pflag.org
PFLAG is a national organization which promotes the health and well-being of GLBT persons and their families and friends through support, education and advocacy. Local PFLAG chapters are active all over the country.

Reconciling Ministries Network
773-736-5526
www.rmnetwork.org
RMN is a movement within the United Methodist Church which seeks to generate a grass-roots response to religious intolerance and to support communities and individuals that advocate justice and human rights for all persons of all sexual orientations and gender identities.

Though it is particular to the UMC, RMN works with similar groups within other denominations and its website contains links to those organizations. Here are just a few for your convenience:

Baptist:
Welcoming & Affirming Baptists (American)
Honesty (Southern) - rainbowbaptists.org
Episcopal:
Integrity - integrityusa.org
Lutheran:
Lutherans Concerned - lcna.org
Presbyterian USA:
More Light Presbyterians - www.mlp.org
Roman Catholic:
Dignity - dignityusa.org
United Church of Christ:
UCC Coalition for LGBT Concerns - www.ucccoalition.org