The choir loft in the rear of the Basilica houses a magnificent, specially-designed 54-rank pipe organ. Built by the Delaware Pipe Organ Co. and installed in 1981, the organhas three mahogany pipe towers, each in an eight-foot semicircle, representing the Holy Trinity. There are 51 pipes in the three towers with the balance of pipes located behind the towers. Pipework is of metal and wood and ranges in length from six inches to 18 feet!

The newer instrument replaced the original custom-made Wurlitzer organ, which had deteriorated beyond repair.