This article interrogates the complicated understanding of sectarianism in institutional cultures in late-nineteenth-century England through an examination of the practice of religion in the daily life of hospital wards in voluntary hospitals. Voluntary hospitals prided themselves on their identity as philanthropic institutions free from sectarian practices. The public accusation of sectarianism against University College Hospital triggered a series of responses that suggests that hospital practices reflected and reinforced an acceptable degree of ‘tolerable intolerance’. The debates this incident prompted help us to interrogate the meaning of sectarianism in late nineteenth-century England. How was sectarianism understood? Why was it so important for voluntary institutions to appear free from sectarian influences? How did the responses to claims of sectarian attitudes influence the actions of the male governors, administrators and medical staff of voluntary hospitals? The contradictory meanings of sectarianism are examined in three interrelated themes: the patient, daily life on the wards and hospital funding. The broader debates that arose from the threat of ‘sectarianism in hospital’ uncovers the extent to which religious practices were ingrained in hospital spaces throughout England and remained so long afterwards. Despite the increasing medicalisation and secularisation of hospital spaces, religious practices and symbols were embedded in the daily life of voluntary hospitals.