We have developed a method for comprehensive analysis of sugar phosphates by high performance anion exchange chromatography with pulsed amperometric detection coupled with a titanium dioxide column as a trap-column to remove sample matrices. Levels of sugar phosphates and a nucleotide phosphate from Arabidopsis thaliana grown at three different inorganic phosphate (Pi) concentrations in nutrient media or from Pi-related Arabidopsis mutants were investigated. Fructose-6-P, Galactose-1-P, Glucose-1-P, Glucose-6-P and Mannose-6-P apparently increased in proportion to increases in the in vivo level of Pi in wild type plants. In contrast, levels of Sucrose-6-P and UDP-Glucose decreased as the in vivo Pi levels increased. Responses of the former sugar phosphates except Mannose-6-P to the in vivo Pi levels in shoots of the mutants were similar in the wild type plants. However, Sucrose-6-P and UDP-Glucose responded differently between the wild type and mutant plants.