Data on deaths in custody reported by the prison administration were matched with data from death certificates in the CépiDc-Inserm national mortality database to study the medical conditions associated with suicides and other deaths occurring in prison. Between 2000 and 2010, 2,613 deaths in custody were reported by the prison administration. The matching process identified 2,541 individuals (97.2%) in the national mortality database. The prison administration recorded 1,219 suicides, while 1,043 suicides were reported on death certificates. Suicide was listed as the cause of death for 982 deaths in both sources. Additionally, for 182 suicides identified by the prison administration, no cause of death was listed on the corresponding death certificate. Based on these two sources, the estimated number of suicides in custody between 2000 and 2010 is between 1,258 and 1,295. Excess mortality due to suicide in custody was observed (an excess mortality ratio [EMR] of 7.3 among men and over 20 among women), while mortality from “natural causes”—excluding AIDS—was lower among incarcerated individuals than in the general French population. In more than half of the death certificates for individuals who died by suicide while incarcerated, no somatic or psychiatric conditions were mentioned; psychiatric conditions, mentioned in only 15.5% of cases, were likely underreported. Establishing epidemiological surveillance of suicides in detention would require reviewing medical records or consulting the health units responsible for the deceased inmate, as well as improved transmission of information from forensic medical institutes to the CépiDc-Inserm.