The Shrine and Parish Church of Holy Innocents was established in 1868. The present edifice was completed in 1870 using the Gothic Revival style of architecture. The first pastor engaged Constantino Brumidi to create a monumental fresco over the main altar. He later decorated the Great Rotunda of the U. S. Capitol Building.

In the early years, cows roamed the streets and open pastures around Holy Innocents. As the city rapidly expanded northward the community, known as the "Tenderloin", teemed with immigrants from Europe. Holy Innocents was called the "actor's church". Eugene O'Neill, the playwright, was baptized in the church in 1888.

In 1890, after the death of the pastor Rev. John Larkin, pastor Rev. Dr. Richard Brennan from St. Rose of Lima's Old Church, New York, since 1875, was transferred to Holy Innocents.

In the 1900s, the area was changed by commerical buildings from newspaper publishing (The New York Herald) to theaters (The Metropolitan Opera House, at 39th St). In the 1920's hundreds of thousands of workers earned their living in what became known as the Garment Center. Longacre Square changed its name to Times Square and Herald Square became synonymous with shopping. Meanwhile, Holy Innocents became spiritual oasis for vast number of people who went to work in the offices, factories and showrooms in the buildings that towered above. Not only did the church continue to offer spiritual direction but it also assisted people to rise to better economic and social circumstances.

Today, in addition to serving as a commuter parish, Holy Innocents offers daily Mass in the extraordinary form of the Roman Rite (the 1962 edition of the Tridentine Mass or Latin, Mass) since 2009.

Priests
Rev. Fr. James L. P. Miara, M. Div., Pastor
Rev. Fr. Louis Van Thanh, Resident Priest
Rev. Fr. Oliver Chanama, Resident Priest
Rev. Fr. Andrzej Bielak, Resident Priest