Various other spellings are used for the old parish (Kilfillan, Kylhelan, Killilellin, Kyllinan, Kilenan, Kilellan and Killallan). The location was the circa seventh century site of the cell of a St Fillan, probably a follower of Saint Columba, whose was held in such reverence that his arm bone was one of the holy relics paraded in front of the Scots Army at Bannockburn. His name in Gaelic means 'little wolf' and his feast day was 9 January. The cult of St Fillan's was introduced by Irish immigrants and the church one of several that Walter fitz Alan, Steward of Scotland gifted to Paisley Abbey in 1169, a foundation that he himself established. Several other St Fillan's sites with churches, wells, seats, etc. exist in elsewhere in Scotland. St Fillan is the patron saint of the mentally ill.
The present parish of Houston and Killellan dates from 1771 when the two parishes of Houston and Killellan were joined. The former parish kirk in the nearby hamlet of Kilallan was known as the Church of St Fillan which gives the hamlet its name. The former church building was left redundant by the unification and was abandoned and un-roofed some time after 1791. The Barochan Aisle on the north side of the kirk is the burial place of the Flemings of near by Barochan Castle, feudal superiors and heritors of the kirk. The ruin carries two datestones, the oldest dated 1635 however the present building is much older dating back to at least the 10th or 11th century, affirmed by the ancient rectangular shape of the kirk. This scheduled monument is now in the care of the Kilallan Kirk Preservation Trust following its donation in 2005 by the Elderslie Estates. An annual service at St Fillan's is held amongst the ruins by the minister and congregation of the united parish.
North and south facing doors may have been the original design in the present building however 17th and 18th century alterations resulted in doors and windows being blocked up with old tombstones, etc. and a new door dated 1635 located in the south wall reflecting post-reformation protocols. A square hole to the left of the door marks the site of the old parish jougs that were stolen, discovered by chance and donated to a local museum who have yet to locate them. A story is told of a woman of short stature who having committed some misdemeanor had the jougs placed around her neck so that she would suffer public humiliation, however she fell off the box she was made to stand on and the short chain resulted in her strangulation.
The church bell bears the inscription "CAROLVS HOG ME FECIT 1618" although it was recast in 1844. It was removed from the kirk and hung in a tree at Barochan House, home of the Flemings of the Fleming Aisle, seeing daily use. The bell is now kept in the parish church and rung once a year before the annual service on the first Sunday in July, the saint's feast day.
A 6th century bronze Byzantine coin and a pewter crucifix of medieval date were found in amongst the ruins of the church. A part of a knight's gravestone, bearing part of a sword, has been found built into the church walls.
The abandoned church saw some degree of maintenance over the years and in 1955 the walls were in good condition and showed signs of being cared for. The church interior was used for burials in the 19th century with the addition of the Barochan Aisle, iron railings partitioning off the east end and plaques mounted on the walls in several places. However the effect of the elements in this exposed location together with plant growth was causing serious damage and an extensive restoration project was undertaken and completed by 2014.
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