Intrauterine growth restriction (IUGR) is a serious pregnancy complication caused by placental insufficiency. We previously reported that truncation of MIMT1 gene exons 3 and 4 (MIMT1Del) causes IUGR in cattle. Here we investigated miRNA expression in the foetal and maternal placenta tissues of MIMT1Del/WT foetuses. Small RNA next generation sequencing and quantitative PCR revealed placental tissue-specific expression of the miR-4321, known to regulate many genes involved in early foetal development. This study also indicated that maternal and foetal components of the placenta respond differently to a deleterious conceptus mutation.