Resumen: Purpose: Although suicide rates of prison populations and incidence factors have been reported for high-income countries, data from low- and middle-income regions are lacking. The purpose of the study was to estimate suicide rates among prison populations in South America, to examine prison-related factors, and to compare suicide rates between prison and general populations. Methods: In this observational study, we collected the numbers of suicides in prison, rates of prison occupancy, and incarceration rates from primary sources in South America between 2000 and 2017. We compared suicide rates among prisoners with incidence rates in the general populations by calculating incidence rate ratios. We assessed the effect of gender, year, incarceration rates and occupancy on suicide rates in the prison populations using regression analyses. Results: There were 1324 suicides reported during 4,437,591 person years of imprisonment between 2000 and 2017 in 10 South American countries. The mean suicide rate was 40 (95% CI 16–65) per 100,000 person years for male and female genders combined. The pooled incidence rate ratio of suicide between prison and general populations was 3.9 (95% CI 3.1–5.1) for both genders combined, 2.4 (95% CI 1.9–3.1) for men and a higher ratio in women (13.5, 95% CI 6.9–26.9). High occupancies of prisons were associated with lower incidence of suicide (β = − 58, 95% CI − 108.5 to − 7.1). Conclusions: Suicides during imprisonment in South America are an important public health problem. Suicide prevention strategies need to target prison populations.