Located at both the East and West ends of the Nave is the Cathedral’s Pipe Organ. During the period of reconstruction in the late 1940’s, this magnificent pipe organ was built and scaled for St. John Cathedral by the Holtkamp Organ Company of Cleveland. It includes 4368 pipes in 72 ranks, distributed among 7 divisions. The west end Galery Organ (54 ranks), located above the main entrance, is 3 times the size of the east end Chancel Organ (18), which is situated behind the Reredos. The organ is playable from 2 three-manual consoles, one located in the loft at the west end and the other behind the Cathedra at the east end.

Below the organ loft, on either side of the nave are statues dedicated to
St. Anthony of Padua and St. Therese of Lisieux.
Next to these shrines, there are also pictures dedicated to the Divine Mercy and Bl. Teresa of Calcutta.