Palles married Ellen Doyle in a Catholic ceremony in Dublin in 1862 and they had one son, also named Christopher (1863-1953). The family lived in Mountjoy Square in Dublin, then moved out to Mountanville in Clonskeagh to a site subsequently named "Knockrabo", where they cultivated a peach orchard, and to 28 Fitzwilliam Place where a town-brick neo-gothic oratory was added (and can still be seen from Leeson Street). According to his biographer, the founding meeting of the Clongowes Union was held in Palles' house in Fitzwilliam Place, with Palles presiding.