Non-Alcoholic Fatty Liver Disease (NAFLD) is the most prevalent liver disorder worldwide, involving pathogenic mechanisms of liver sinusoidal endothelial cells (LSECs), hepatocytes and other liver cells. Here, we used a novel approach of label-free Raman confocal imaging to study primary LSECs and hepatocytes freshly isolated from the livers of mice with NAFLD induced by a high fat diet (HFD), in comparison to healthy controls. Our aim was to characterize changes in the biochemical composition in LSECs and hepatocytes that occur in a single cell at the subcellular level. LSECs from NAFLD livers displayed a significant increase in the intensity of marker bands of nuclear DNA that was not associated with changes in LSEC nucleus size. A number of changes in the cytoplasm of hepatocytes were identified. However, the most prominent change in hepatocytes was a substantial increase in the degree of unsaturation of LBs' (lipid bodies) lipids in NAFLD, suggesting an increase in the de novo lipogenesis of unsaturated lipids. The confocal Raman imaging of single live cells isolated from the liver provided a unique tool to better understand disease-induced cell-specific changes in the biochemical phenotype of primary liver cells.