A document from Bishop Rüdiger von Passau dating from 1243 indicates that the church was a subsidiary of St. Martin in Klosterneuburg.
At the time, the parish of Heiligenstadt also covered the neighbouring communities of Grinzing, Sievering, Salmannsdorf, Nussdorf, Oberdöbling and Unterdöbling.
In 1745, Cardinal Sigismund von Kollonitz donated an artefact belonging to Saint Severinus to the church, which has been revered as a holy relic ever since.
During an archaeological dig in 1952–53, the remains of a Roman building were uncovered beneath St. James's Church.
The Roman ruins lay within the bounds of the church and sometimes beyond; the building had been destroyed twice and houses two early Christian graves.
[1] Earlier theories that the modern name is a reference to the grave of Saint Severinus have been rejected by more recent research.