The consumption of berries has been linked to decreased risk of degenerative disease. Berries are regularly processed into juices. It is largely unknown how the juicing process affects the bioavailability of metabolites. As metabolomics has shown to be a valuable nutritional tool to study global metabolite differences, the aim of the present study was to investigate the effect of juicing on the relative appearance of blueberry metabolites in humans using metabolomics. Nine healthy subjects consumed 250g of fresh blueberries either as the whole fruit or following juicing, and provided blood and urine samples before and 2h following intake in a crossover design. Samples underwent metabolite profiling using LCMS, and data was mined with multivariate analysis. Overall, less than 12% of all ions detected were significantly influenced by blueberry treatment (P<0.05). PLS-DA models of post treatment samples revealed good discrimination. In urinary samples, whole blueberry treatment resulted in 108 ions that were significantly higher compared to juiced treatment (positive and negative mode combined) while only 8 were significantly higher following juiced treatment. Examples of putative annotations included metabolites of ferulic and caffeic acids, several phenolic metabolites conjugated to sulfate, glycoside or glucuronide and fatty acyl derivatives, which were higher intensity following whole blueberry treatment. In conclusion, consumption of whole blueberries resulted in a higher range of phenolic and other metabolites in plasma and urine samples 2h following consumption. Both whole and juiced blueberries resulted in very similar metabolite profiles at 2h although this was the only time point measured.