The organ at the Church of the Transfiguration is a revitalization and expansion of components from organs built in America by the E. M. Skinner Organ Company in the early 20th century. When completed, approximately 12,500 pipes will resonate from the north and south side aisles in a unique design by Nelson Barden Associates of Boston.

The South Great Division of the organ has been completed by Nelson Barden & Associates and is presently in storage. It will be installed after the largest pedal pipes are placed in position on the south platform.

The organ has outgrown the existing console and specifications for a new console are being developed. Currently, the organ consists of the Great, Swell, Choir, Processional, and Pedal divisions, a total of 88 ranks. The Echo division of 31 ranks has been installed and will be playable on the new console, which is being designed for completion in 2010.