Background: Long non-coding RNAs (lncRNAs) play important roles in cellular processes and disease pathogenesis. In this study aimed was to investigate the association between expression levels of BAT5 and IL21R-AS1 as two candidate lncRNAs and acute myocardial infarction (AMI). Methods and Results: In this case-control study, the relationship between AMI and expression levels of BAT5 (HLA-B-Associated Transcript 5) and IL21R-AS1 (IL21R antisense RNA 1), in 231 patients who underwent percutaneous coronary interventions were investigated. Expression levels of lncRNAs in leukocytes were measured by quantitative real-time PCR (qRT-PCR). The m 6A modification regions and subcellular localizations of these lncRNAs were predicted by in silico analysis. Ranked ANCOVA tests were used to compare expression levels of lncRNAs between groups after adjusting for gender and use of cardiovascular drugs. The crude and adjusted expression levels of BAT5 and IL21R-AS1 in leukocytes of AMI patients (n=128) were found to decrease compared to the control cases (n=103) (p<0.01 and p<0.05, respectively). The intracellular functional localization of both lncRNAs is non-nuclear. The number of high confidence m 6A modification regions of BAT5 and IL21R-AS1 transcripts was determined as 5 and 4, respectively. Conclusion: This study indicates that MI patients are associated with decreased expression levels of BAT5 and IL21R-AS1 in leukocytes compared with controls and may have an impact on myocardial infarction pathogenesis in the acute phase.