Storage losses of sugar beets are affected by storage conditions, but may also depend on growing site and genotype. The aim of the present study was to quantify the genotype effect on storage losses and to analyze the reasons for genotypic variability in sugar losses and accumulation of invert sugar. In 2011, 36 sugar beet genotypes and in 2012, 18 genotypes were cultivated at two growing sites. After harvest beets were stored for 8 and 12 weeks at 8 °C and 20 °C in climate containers, respectively. Sugar losses increased with thermal time in store and were closely related to invert sugar accumulation. The growing site strongly affected the storage losses and maximum genotypic differences occurred at growing sites with particularly high level of storage losses. Genotypic differences were primarily caused by differences in the level of infestation with microorganisms, but also by differences in the beets’ carbohydrate metabolism. The infestation with microorganisms after storage was related to the marc content of genotypes before storage pointing to a non-specific resistance. The results underline a marked influence of the genotype on storage losses with a proportion of variance of 12%. Thus, selection of varieties with improved storability seems promising to reduce storage losses of sugar beet. But so far, no criteria are available to select for good storability of sugar beet varieties.