The invention is a disease diagnosis system (100), wherein the disease of a test individual is predicted based on metabolomic measurements taken from the said test individual. Accordingly, it comprises a processor unit (110), characterized in that the said processor unit (110) is configured to perform the following steps: accessing a metabolic network model (121) stored in a memory unit, wherein a metabolic network (400) comprising a plurality of metabolic pathways (410) identified by metabolites and metabolic reactions (412) in which metabolites and metabolites (411) are involved； accessing a reference database (122) in which the metabolite (411) fold-change values of said individuals are stored in relation to the reactions (412) involving the metabolites (411) for each of the healthy individuals and the diseased individuals associated with at least one disease； determining an average metabolic flux value for each metabolic pathway (410) in the metabolic network model according to the metabolite (411) fold change values in the reference database (122)； generating a set of metabolic flux values for each individual in the reference database comprising individual-specific minimum and maximum metabolic flux values of each metabolic pathway (410) in the metabolic network model (121)； generating a set of reference difference values for each individual according to the deviations of said metabolic flux value sets from the average metabolic flux values； receiving test data of the fold-change values of the metabolites (411) in the metabolomic measurements taken from said test individual as input； associating the metabolites (411) in the test data with the metabolic pathways (410) containing the reactions (412) of said metabolites and determining a minimum and maximum metabolic flux value for each of the metabolic pathways (410)； generating test difference values according to the deviations of the determined metabolic flux values from the average metabolic flux values； apply
