Long-term fructose consumption has been shown to evoke leptin resistance, to elevate triglyceride levels and to induce insulin resistance and hepatic steatosis. Autophagy has been suggested to function in processes such as lipid storage in adipose tissue and inflammation in liver. Autophagy and the leptin system have also been suggested to regulate each other. This study aimed to identify the changes caused by fetal undernourishment and postnatal fructose diet in the gene expression of leptin, its receptors (LEPR-a, LEPR-b, LEPR-c, LEPR-e and LEPR-f) and autophagy genes in the white adipose tissue (WAT) and liver of adult male rats in order to clarify the mechanism behind the metabolic alterations. The data clearly revealed that the long-term postnatal fructose diet decreased leptin levels (p<0.001), LEPR (p<0.001), especially LEPR-b (p=0.011) and LEPR-f (p=0.005), as well as SOCS3 (p<0.001), ACC (p=0.006), ATG7 (p<0.001), MAP1LC3β (p<0.001) and LAMP2 (p=0.004) mRNA expression in WAT. Furthermore, LEPR (p<0.001), especially LEPR-b (p=0.001) and LEPR-f (p<0.001), ACC (p=0.010), ATG7 (p=0.024), MAP1LC3β (p=0.003) and LAMP2 (p<0.001) mRNA expression in the liver was increased in fructose-fed rats. In addition, the LEPR expression in liver and MAP1LC3β expression in WAT together explained 55.7% of the variation in the plasma triglyceride levels of the rats (R adj. (2) =0.557, p<0.001). These results, together with increased p62 levels in WAT (p<0.001), could indicate decreased adipose tissue lipid storing capacity as well as alterations in liver metabolism which may represent a plausible mechanism through which fructose consumption could disturb lipid metabolism and result in elevated triglyceride levels.