Abstract: Background and Objective: Molecular mechanisms of most anti-obesity drugs are remained to be clear. MicroRNAs that are noncoding RNA molecules supposed to regulate biological processes concomitant to obesity and have attracted a lot of attention to themselves. The miR-27a and miR-143 expression levels in obese and non-obese rats during weight changes and L-carnitine (LC) effects on them was investigated in this study. Materials and Methods: In the present study 12 male Wistar rats were randomly divided into normal fat diet and high fat diet groups to develop obesity. After 8 weeks rats were weighted and half of diet induced obese rats were randomly selected to receive 200 mg LC kg–1 b.wt. for 4 weeks. At the end epididymal fat was isolated to investigate expression level of microRNAs by real-time PCR. Results: After 12 weeks, high fat diet in comparison with normal fat diet mediated significant decrease and increase in expression levels of miR-27a and miR-143 , respectively. These changes were modified in groups, which had received LC in a 4 weeks period. Furthermore, rats in this group gained less weight. Conclusion: Findings of this study suggest that the changes of microRNAs expression probably play a role in pathogenesis of obesity, might be modulated by means of dietary agents and supplements and modify weight gain trend.