Introduction: Maternal obesity and diabetes are increasingly prevalent during pregnancy and may have long-term consequences on the offspring’s health. Currently, metformin (MET) is prescribed to treat gestational diabetes but its impact on the developing fetus is unknown. In mice, maternal obesity during pregnancy results in altered blood pressure and heart size in the adult offspring. It remains to be determined whether such changes have their origins during fetal development and what effects maternal MET has on fetal hearts. MicroRNAs (miRNA) are implicated in cardiac differentiation and remodelling and affect the susceptibility to cardiovascular diseases. We therefore investigated whether high fat (HF) diet-induced maternal obesity with or without MET alters miRNA expression and expression of the target mRNAs within the fetal heart, which may underlie the postnatal cardiovascular phenotype. Methods: Female C57/BL6J mice were fed either a HF (45% kcal fat) or control (C, 7% kcal fat) diet six weeks prior to conception and during pregnancy, with half of HF and C dams given MET in drinking water (250mg/kg bodyweight/day) throughout pregnancy. This generated four dam groups (n=4 per group): C, C+MET, HF and HF+MET. On day 16 of pregnancy dams were killed and fetal hearts taken for analysis. MicroRNA expression was measured using small RNA sequencing (Illumina miRNA-Seq, Expression Analysis, USA). Differential expression analysis identified both up and down-regulated miRNAs (p<0.05) and pathway analysis was carried out using DIANA miRPath. Expression levels of the circadian clock genes Clock, Bmal1, Per2 and Cry2 were measured by quantitative real-time PCR. Data were analysed using two-way ANOVA. Results: 33 miRNAs were expressed differentially in hearts of fetuses from C vs HF dams, while 48 miRNAs were expressed differentially in hearts of fetuses from C vs C+MET dams. On the other hand, 71 miRNAs were expressed differentially in hearts of fetuses from C vs HF+MET dams. Pathway analysis identified circadian rhythm as a potential micoRNA regulated gene pathway that is altered by both maternal obesity and metformin. Maternal obesity reduced fetal heart mRNA expression of the clock genes Per2 and Cry2 (p<0.05) vs those from lean mothers. Conclusion: This study identified miRNAs that alter the circadian rhythm pathway in fetal hearts in response to maternal obesity. The circadian genes Per2 and Cry2 are targets of these microRNAs. This suggests that maternal obesity during fetal development could alter the expression of miRNAs and their target genes in fetal heart, and this may underlie the associated cardiovascular dysfunction in postnatal life.