This study conducted a comparative analysis of fatty acids (FAs) concentration derived from polar (PL) and non-polar (NPL) lipids in the liver and muscle tissues of rats and mice. The objective was to elucidate species-specific differences in tissue FA distribution. Employing targeted GC/MS-based methodology, the study aimed to provide insights into conserved and species-specific aspects of lipid metabolism, thereby enhancing future experimental design, linked with comprehension of the interactions between diet, metabolism, and health. Results revealed markedly higher levels of total fatty acids (TFAs) derived from PL in mice skeletal muscle compared to rats and elevated saturated fatty acids (SFAs) levels in mice. Unsaturated fatty acid levels, mainly monounsaturated fatty acids (MUFAs) and polyunsaturated fatty acids (PUFAs), were substantially higher in mice muscle across all lipid classes, resulting in a higher PUFA/TFA ratio in mice muscle. Detailed analysis of specific unsaturated fatty acids (C16:1, C18:1n9c, C18:2n6c, C22:6n3) indicated elevated levels in mice relative to rats. Conversely, rats exhibited higher SFA levels derived from the NPL fraction in the liver, particularly in myristic (C14:0), stearic (C18:0), and tricosanoic (C23:0) acids. Mice liver PL fractions displayed significantly elevated unsaturated FA levels, with notably higher MUFAs and lower PUFAs in NPL fractions compared to rats. Analysis of specific unsaturated FAs revealed higher levels of palmitoleic acid (C16:1) in mice, while rats exhibited increased linoleic (C18:2n6c) and linolenic (C18:3n3) acids. In conclusion, significant differences in FAs tissue distribution between rats and mice underscore the importance of considering species-specific FAs variations when utilizing these animal models and interpreting experimental results related to FA metabolism.