The Church of the Intercession houses one of the finest American pipe organs in Harlem in all of New York City. This is the second instrument for the church, which was built between 1911 and 1915. The first organ was built by the Austin Organ Company of Hartford, Connecticut. It was a 4 manual with 110 ranks. During this time, the pipes in the facade (the one that you see) were "speaking" pipes (the ones you heard.)

In 1967, the Austin stopped working. Intercession was still a chapel to Trinity Church Wall Street. St. Paul's Church, Fulton Street began plans for a new organ. The present organ, built by Aeolian Skinner, was still working and plans were made to move it up to Intercession.

The Schlicker Organ Company of Buffalo, New York, won the bid to move the instrument. The provided a new console and additional pipe work.

In 1968, the New Intercession organ was complete. Ninety percent of the pipe work is Aeolian Skinner. It is 71 ranks with a 3 manual console. The style is called "American Classic."

The organ case, designed by architect Bertram Goodhue, is in the style of the organs of Spain. The trumpet pipes that fan out from the case is typical of the organs in Seville and Madrid. This design was the first of its kind in America. The pipes are not "speaking" pipes.

The original console was purchased by Riverside Church and is housed in the second gallery of the nave today.