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In Switzerland, the highest rates of suicide are observed in persons without religious affiliation and the lowest in Catholics, with Protestants in an intermediate position. We examined whether this association was modified by concomitant psychiatric diagnoses or malignancies, based on 6,909 suicides (ICD-10 codes X60-X84) recorded in 3.69 million adult residents 2001–2008. Suicides were related to mental illness or cancer if codes F or C, respectively, were mentioned on the death certificate. The protective effect of religion was substantially stronger if a diagnosis of cancer was mentioned on the death certificate and weaker if a mental illness was mentioned.