Data on deaths in custody provided by the prison administration were matched with data from death certificates in the CépiDc-Inserm national mortality database in order 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 recorded for 982 deaths in both sources. Furthermore, for 182 suicides identified by the prison administration, no cause of death was noted in 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 found (SMR 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 pathology was mentioned; psychiatric pathologies, 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 healthcare units responsible for the deceased inmate, as well as improving the transmission of information from forensic institutes to the CépiDc-Inserm.