The original High Altar, c1868 to 1897, was made of wood and was adorned with paintings of the Blessed Virgin, St Joseph, St Patrick and St Brigid, with a pelican motif in the centre panel. It was transferred to a church in Carlton.
The High Altar we see today arrived in 1896, and was designed by Wardell. Set on a foundation of brickwork and concrete, it is made of Emperor Red marble, one of the rarest of Spanish marbles. It features eight coupled columns of Irish green marble and is panelled with mosaic portraits of the Blessed Virgin, the Saviour and St Joseph. The altar itself is 3.04m in length and weighs 2540 kilograms.
The reredos is made of the same red Spanish marble as the altar. An alabaster frame, richly carved in a Gothic design, surrounds the tabernacle. Its pinnacle rises to a height of 7.62m from the floor of the sanctuary. The original tabernacle doors were badly damaged by vandals, and were replaced in 1934.
The altar rails and gates, designed by Wardell, were decommissioned in 1970 and are now in the keeping of the Melbourne Diocesan Historical Commission.