Transcending Boundaries grew out of a project of BiNet USA, a national bisexual organization. Throughout the 1990's, BiNet helped bisexual activists around the country organize on a local level. They sponsored regional conferences, including one in the Connecticut/New Jersey/New York Tri-State Region.

In 2000, BiNet replaced its regional focus with a more centralized organizational style. Those in attendance at the 2000 Tri-State Conference voted to continue the conference independently from BiNet USA and to hold the next year's conference in New Haven, Connecticut.

The organizing committee expanded the scope of the conference in two ways: widening the geographical reach to include the entire Northeastern United States, and including transgender and intersex issues as well as bisexual ones in the conference theme. The new name “Transcending Boundaries” reflected this expanded scope, as well as the fact that bisexuals, transgender persons, and intersex persons do not fit into the simple categories of gay/straight, man/woman, and male/female.

Transcending Boundaries, Inc. was founded in 2001 to organize based on this expanded vision: a Northeast regional conference for bisexual, transgender, and intersex people and our allies. In 2009, this focus was expanded to include the polyamorous community as well. Transcending Boundaries has held five successful conferences between 2001 and 2006, teaming up with the Americas Conference on Bisexuality in 2005 and PFLAG Northeast in 2006. After a brief absence, Transcending Boundaries returned in 2009 and is thrilled to continue its work again in the queer community.

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