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Phosphate groups are naturally present in starch at C3- or C6-position of the glucose residues and impact the structure of starch granules. Their precise quantification is necessary for understanding starch physicochemical properties and metabolism. Nevertheless, reliable quantification of Glc-3-P remains laborious and time consuming. Here we describe a capillary electrophoresis method for simultaneous measurement of both Glc-6-P and Glc-3-P after acid hydrolysis of starch. The sensitivity threshold was estimated at the fg scale, which is compatible with the analysis of less than a $\mu$g of sample. The method was validated by analyzing antisense potato lines deficient in SBEs, GWD or GBSS. We show that Glc-3-P content is altered in the latter and that these variations do not correlate with modifications in Glc-6-P content. We anticipate the method reported here to be an efficient tool for high throughput study of starch phosphorylation at both C3- and C6-position.