Capillary electrophoresis (CE) equipped with a diode-array detector, and GC-MS have been used to determine diagnostic metabolites occurring in urine of patients with various metabolic disorders. The urine samples were injected directly onto the CE instrument without any pretreatment. GC-MS required extraction and derivatisation before separation. Identification of abnormal metabolites was based on migration times and characteristic diode-array spectra, or mass spectral library search when GC-MS was used. The CE method has previously been shown capable of diagnosing several metabolic diseases, and was now used on more difficult cases. CE readily diagnosed glyceric aciduria and the secondary metabolite in lysinuric protein intolerance, orotic acid. Methylmalonic aciduria required pressure elution in addition to high voltage to accomplish diagnosis. In mevalonic aciduria the characteristic metabolite had weak light absorption and the mevalonate peak also co-eluted with endogenous aromatic acids making diagnosis difficult. Both in the latter case and with the disorders glutaric aciduria I and glyceroluria, GC-MS was the method of choice. A possible role of CE in the routine system for diagnosing metabolic disorders, might be to use this method for pre-testing all urine samples. Samples with abnormal CE-profiles would subsequently be given high priority for more elaborate analysis with GC-MS and amino acid analyzer. In a different project a CE instrument designed for serum protein analysis was used to study sera from patients with myelomatosis. The method also allowed identification of the various immunoglobulins using immunosubtraction. Samples collected after diagnosis as well as many years prior to disease were available through the Janus-bank. This large serum bank comprises samples collected since 1973 at intervals from nearly 300000 blood donors. It was found that the monoclonal immunoglobulins characteristic of the disease started to appear in serum up to 15 years before clinical diagnosis.