The organ in the sanctuary was designed and constructed by Patrick J. Murphy and Associates, Inc. of Stowe, Pennsylvania. The organ, installed in 2005, is a three-manual, 38-stop instrument. Some original pipes were retained from the former organ, built by M.P. Möller, Inc. in the 1920s.

The tonal design of the Murphy organ is reminiscent of English Romanticism. Features include a partially enclosed Great, 8' Harmonic Flute, 16' wood Violone, and a large scale high pressure "Willis" style Tuba playable on the Choir at 8' and Pedal at 16'.

New Blackington-style slider wind chests were constructed for the main manual stops; most unit chests are electro-pneumatic in design. The drawknob console, constructed of oak and cherry, features E.M. Skinner-styled keyboards and toe stud pistons.

Multiple levels of memory with transposer and record/playback features provide the necessary flexibility to successfully and authentically accommodate repertoire from all musical epochs and genres.

The organ in our All Saints Chapel was built in 1986 by Thomas Eader--a member of St. Mark's and a builder of organs known for his expertise in early instruments. It is a one-manual tracker instrument decorated in the Renaissance Florentine style.