Background: Early detection of stress fractures can be difficult using clinical imaging techniques. MicroRNAs (miRNA) could be used as potential diagnostic biomarkers. Objectives: To establish a miRNA profile associated with increased risk of stress fractures in Thoroughbred racehorses in training. Study design: Prospective case-controlled study. Methods: Residue blood samples from lame Thoroughbreds referred for nuclear scintigraphy and divided into lame stress fracture (5 horses) or lame non-stress fracture (5 horses) groups. A second control group consisted of non-lame Thoroughbreds presenting for blood sampling (5 horses). Next generation sequencing of miRNA profiles was compared between the three groups. The effects of selected stress fracture-related miRNAs on equine bone marrow derived mesenchymal stem cells (BMMSCs) were investigated. BMMSCs were transfected using miRNA-486-5p mimic or inhibitor and a lipofectamine control from three donors. Results: No miRNA profile was identified for potential usage as a biomarker for differentiating stress fracture from lame cases. However, the miRNA profiles of lame cases and non-lame control horses were significantly different. RNA-sequencing showed three miRNAs (eca-miR-486-5p, eca-miR-26a and eca-miR-23a) were differentially expressed (p value <0.05) between lame cases and non-lame controls, which was validated by qPCR. Of these, eca-miR-486-5p demonstrated the most abundant change. Cell transfection experiments using the miR-486-5p mimic treatment in equine BMMSCs showed upregulation of the osteogenic transcription factor, Runt-related transcription factor 2 (RUNX2) and insulin-like growth factor type 1 (IGF1). A significant decrease of miR-133a in the miR-486-5p mimic treated cells was also demonstrated. Main limitations: Small sample size. Exercise can influence miRNA expression was not controlled for between groups. Conclusions: Since RUNX2 is the known target of miR-133a, miR-486-5p together with miR-133a would suggest the biological importance of bone turnover and osteogenesis in equine BMMSCs, but further investigation of role of miR-486-5p and miR-133a in equine bone biology is warranted.