A rapid fractionation method for determination of metabolite levels in the chloroplast and the extrachloroplast compartment of Chlamydomonas reinhardtii has been developed. Protoplasts containing one large chloroplast were fractionated by passing them through a multilayer gradient containing digitonin, polyacrylamide, and a mixture of silicone oil and bromodecane. Lysis of the plasma membrane and the separation of the chloroplasts from most of the extrachloroplast material was achieved within less than 5 s. The chloroplast enriched fraction was contaminated with 3% fumarase (mitochondria) and 13% phosphoenol pyruvate carboxylase (cytosol). Metabolites of the upper glycolytic chain were detected mainly in the chloroplasts, whereas 2-phosphoglycerate was found only in the extrachloroplast compartment. Analysis of changes in metabolite concentrations after transition to anaerobic conditions in the dark pointed to a regulation of carbohydrate catabolism by chloroplast phosphofructokinase and by cytosolic pyruvatekinase.