Individuals in contact with the criminal justice system are a key population of concern to public health. Record linkage studies can be useful for studying health outcomes for this group, but the use of aliases complicates the process of linking records across databases. This study was undertaken to determine the impact of aliases on sensitivity and specificity of record linkage and how this affects ascertainment of mortality. Records for a cohort of prisoners were linked to methadone maintenance treatment (MMT) and mortality records. The record linkage was conducted in two stages. First, the linkage was undertaken using the participant's name and date of birth as recorded in a prior study. Then, a second linkage was undertaken using these identifiers, plus all known aliases. Sensitivity was 64%, and specificity 100%, for the first linkage. When aliases were added to the linkage, sensitivity increased to 86% and specificity remained 100%. The standardized mortality ratio was 4.3 for the first linkage, increasing to 6.1 when aliases were used. These results suggest that the potential effects of participant aliases on linkage outcomes, and methods for mitigating these effects should be carefully considered when planning and undertaking record linkage studies with criminal justice populations.