Aims: A transposition of the long segment of distal ileum in obese Zucker rats improved glucose tolerance 6 months after IT. It was undertaken to compare the gene expression of miRNA-103, -107 and caveolin-1 in the liver of euglycemic groups of IT relative to SHAM operated rats. Main methods: Obese, male Zucker rats underwent either transposition of 50% distal ileum or sham surgery. For determining the gene expression, the Real-Time PCR for caveolin-1 and miRNA-103, -107 was performed. Plasma concentrations of LDL, HDL, TG and total cholesterol were measured with enzymatic colorimetric assays after optimization procedure. Key findings: The Cav-1 expression in liver tissue after ileal transposition was 1.22 times higher compared to the SHAM group (SHAM median 63.58, min 41.3, max 82.4; IT median 77.35, min 60.8, max 95.41, p < 0.001). miRNA-107 expression was significantly downregulated by 0.6-fold in the IT group compared to the SHAM group (SHAM median 507.51, min 236.42, max 721.29; IT median 355.2, min 278.15, max 478.15, p < 0.015. The level of TG was significantly higher after IT surgery (SHAM median 115, min 96, max 143; IT median 153, min 115, max 162, p = 0.001). The total cholesterol plasma levels decreased after IT (SHAM median 178, min 161, max 183; IT median 128, min 103, max 114, p < 0.000001). The LDL plasma level in IT was two-fold lower than in the SHAM (SHAM median 117, min 68, max 151; IT median 58, min 45, max 61, p < 0.000001). Significance: The transposition of 50% of the distal ileum lead to an increase in caveolin-1 and reduction in miR-107 expression compared to those of SHAM group. Endogenous miR-107 is more involved in regulation of the functions of insulin-target liver tissue than miRNA-103. Reduced LDL and cholesterol plasma levels suggest positive effects on lipid metabolism in long-term observations. The present study is the first to show a lack of IT effect regarding triglycerides six months after surgery.