The Glembotski lab has previously demonstrated that ischemia/reperfusion (I/R) injury causes an accumulation of misfolded proteins in the endoplasmic reticulum (ER) of cardiac myocytes. Misfolded proteins are sensed by the ER transmembrane protein, activating transcription factor 6 (ATF6), which subsequently upregulates a canonical cardioprotective gene program that restores ER protein homeostasis (proteostasis). In addition to canonical ER-resident targets, RNA sequencing analysis of ATF6 transgenic mouse hearts has revealed putative induction of the gene that encodes the peroxisomeresident protein, fatty acyl-CoA reductase 1 (FAR1). Since FAR1 is the rate-limiting enzyme in plasmalogen synthesis at the peroxisome, this finding suggests a new role for ATF6 in regulating peroxisome function in the heart. While plasmalogens comprise a significant portion of phospholipids in the heart, and have been postulated to have deleterious effects during oxidative stress, peroxisome function, and by extension plasmalogen synthesis, has yet to be studied in the heart. Despite numerous studies on peroxisomes in various tissue types, the existence of functional peroxisomes in the heart has yet to be comprehensively established. Here, functional peroxisomes were identified in cardiomyocytes by visualizing co-localization of the known peroxisome markers, PMP70 and catalase, and assessing the integrity of the peroxisome-import machinery. Further, the present study addresses whether ATF6 regulates FAR1 in cardiomyocytes, and elucidates the effect of FAR1-mediated plasmalogen synthesis under basal and I/R conditions. Using adenovirus (AdV) encoding forms of ATF6 exhibiting different transcriptional activities, FAR1 was induced by these ATF6 AdV in a manner similar to canonical ATF6 target genes in cardiomyocytes. Moreover, FAR1 was induced during ER stress in an ATF6-dependent manner, supporting the hypothesis that FAR1 is an ATF6-inducible ER stress response gene. Using FAR1 loss-of-function maneuvers, FAR1 was shown to be required for basal myocyte viability but, remarkably, exacerbated cell death during simulated ischemia/reperfusion (sI/R), indicating plasmalogens may exert cardioprotective effects under basal conditions, but have a detrimental role during I/R. Taken together, this is the first study to comprehensively demonstrate the existence of functional peroxisomes in cardiomyocytes, and establish an unexpected role for ATF6 in regulating FAR1-mediated plasmalogen synthesis, and therefore peroxisome function, in a maladaptive manner during I/R.