Somatic cell nuclear transfer (SCNT) has been successfully undertaken in 17 mammalian species, however the efficiency of this technique remains low (less than 5%) for most species, except for cattle, with a live birth rate of up to 15%. The main factor associated with low efficiency has been perturbed nuclear reprogramming of cloned embryos. Since microRNAs (miRNAs) play an important role in cell reprogramming and embryo development, differences in their expression profile may underpin issues with nuclear reprogramming. The aim of this study was to investigate whether differences exist in the miRNA expression profiles of bovine blastocysts produced via IVF compared with SCNT. A total of 120 blastocysts were produced via IVF (n=60) using female sexed semen (n=60; n>3 cultures) or SCNT using a donor female fibroblast cell line (n=60; n>3 cultures) were collected on day 8 of development, total RNA extracted, and small RNA library prep and sequenced conducted on an Illumina NovaSeq™ X system (150bp, paired-ended). Illumina data files were processed, and differential expression analysed using DeSEQ2 on the online Galaxy Australia platform. A total of 268 expressed miRNA were identified. Of these, 20 differed significantly (FDR<0.05), including 9 up-regulated and 11 down-regulated in SCNT compared with IVF embryos. Those miRNAs were associated with different biological processes, including cell proliferation and apoptosis. These findings describe differences in the miRNA profile of IVF and SCNT-derived blastocysts in cattle. Further studies are required to confirm the exact function and effect of these 20 differentially expressed miRNA on embryo development, as these miRNAs may explain the different developmental potential of bovine blastocysts produced by SCNT.