The objective of this work was to develop a sample preparation procedure for determination of the carbohydrate profiles in commercial juice samples by three principally different analytical methods: capillary electrophoresis (CE) with indirect detection, high-performance liquid chromatography (HPLC), and matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS). The preparation and purification of juice samples prior to analysis is described. The method using Carrez reagents was found to be an efficient preparation tool for all three methods. The addition of Carrez reagents to the samples for mass analysis improved the quality of the mass spectra of oligosaccharides. The amounts of glucose, fructose, and sucrose as major carbohydrates in fruit juices measured by CE using a simple instrument are in good agreement with the HPLC values and the data declared by the producers of the juices. The results from both methods are critically evaluated and their impact for studies of authenticity is discussed. The decrease of sucrose amount during the storage of samples was explained by acid hydrolysis of this disaccharide.