Introduction Mortality is substantially increased among those who have been imprisoned but there is little information about the extent to which excess mortality might be explained by deprivation. All cause mortality among Scottish prisoners has not previously been described.

Methods Standard record linkage methods were used to link Scottish Prison Service and mortality data for individuals imprisoned in Scotland for the first time between 1 January 1996 and 31 December 2007.

Results Among 76 627 individuals there were 4414 deaths (3928 in men). Compared to the general population the RR of mortality (adjusted for age and year of death) was 3.3 (95% CI 3.2 to 3.4) for men and 7.5 (6.8 to 8.2) for women. Further adjustment for deprivation accounted for part of this excess (adjusted risks 2.3 (2.2, 2.4) and 5.6 (5.1, 6.1) for men and women respectively). RRs were highest for drug and alcohol related causes, suicide and homicide and were markedly higher among women than men for these causes. Out of prison death rates were highest in the first week after discharge from prison. Mortality rates were lower in those with longer total duration in prison and higher in those with more episodes in prison.

Conclusions People who have been imprisoned in Scotland experience substantial excess mortality that is only partly explained by their levels of deprivation. The association of increased mortality with multiple shorter periods in prison and the concentration of deaths in the early period after prison discharge have substantial implications for policy and practice.