Background Mental illness and substance abuse have been increasingly linked to criminal justice system involvement, but this relationship has mostly been by survey of prison populations and inferences of excess rates of disorder made by noting how these rates compare with national population‐based surveys of mental disorders. Aims The aim of this study is to examine associations between history of mental disorders, including substance misuse, with incarceration history within a single population‐based data set. Methods Data were from the National Comorbidity Survey Replication, a nationally representative household survey of respondents 18 years and older conducted between 5 February 2001 and 7 April 2003. Results Multivariate regression analysis showed the strongest independent risk factors for a history of incarceration were being male [odds ratio (OR) = 6.3; p < 0.001], past receipt of welfare payments (OR = 2.1; p < 0.001), longer than 1 week of past homelessness (OR = 2.1; p < 0.001), not being from the northeast of the USA (OR = 0.31; p < 0.001) and a lifetime substance abuse or dependence diagnosis (OR = 4.9; p < 0.001). With the exception of welfare payments, these measures were also independently associated with longer (27 + days) incarceration. Conclusions The socioeconomic associates of incarceration history were unexpected, and in line with other, differently conducted studies. The fact that only substance misuse disorders of all those assessed were independently associated with incarceration history was a surprise, given the multiplicity of prison surveys, which have shown higher rates of other serious mental disorders. Although we were unable to include measures of schizophrenia or similar psychosis and used impulse control disorders as surrogates for personality disorder, absence of a relationship between depression and incarceration when measured in the same way and over the same time among those previously incarcerated and those not, raises questions about the weight that should be put on the existing epidemiological perspective of mental disorder among prisoners. Published 2013. This article is a U.S. Government work and is in the public domain in the USA. Criminal Behaviour and Mental Health published by John Wiley & Sons Ltd.