Conjugated linoleic acids (CLA) have been extensively advertised as dietary supplements to reduce fat and increase muscle mass. However, the role of CLA in glycogen metabolism is still largely unknown. The aim of this study was to assess the effect of CLA on glycogen synthesis in vitro (CCL 136 cell line human) and CLA in vivo (C57BL/6J mice). The materials used were the CCL 136 muscle cell line and muscles of female C57BL/6J mice (n = 52), housed at animal laboratory facility and feed with "MURIGRAN", a standard feed prepared for rodents (Agropol, Poland). Chemically pure fatty acids were added to soybean oil. CLA isomers (c9,t11 CLA, t10,c12 CLA, and as a mixture (1:1)) were administered with feed. Supplementation in mice started at week 6 of age and lasted for 4 weeks. Methods used in the study were real time- PCR - quantification of gene expression, Western blot glycogen synthase kinase-3 (GSK3α 9) and glycogen synthase (GS) protein, glycogen staining by PAS. Quantitative determination of glycogen by spectrophotometry and intracellular reactive oxygen species was measured the intracellular oxidation of dichloro-dihydro-fluorescein diacetate (DCFH-DA). In vitro data showed that GS and GSK3 expression was lower in cells cultured with different CLAs and a mixture of CLAs. GS gene expression was significantly decreased in cells cultured with c9, t11 CLA (P < 0.04) and t10, c12 CLA (P < 0.05) as well as the mixture of both isomers. The GSK3α gene expression was reduced in cells cultured with a mixture of CLA (P < 0.02), whereas phosphorylation of GSK3α increased in cells cultured with c9, t11 CLA GSK3α (P < 0.05). In vivo data showed a reduction in the glycogen concentration among mice fed a diet containing t10, c 12 CLA and a mixture of CLA isomers. We conclude that both CLA isomers can affect the synthesis of glycogen in muscle cells through the regulation of GS and GSK3α gene expression.