A flow injection (FI) system with a mini-immunoaffinity chromatographic column was used to perform on-line assays of specific proteoglycans. The 300-microL mini-column contained beads coupled with monoclonal antibodies against the specific sulfation pattern of chondroitin sulfate proteoglycans, which have been reported to be a potential biomarker for cancer. The amount of these proteoglycans present was estimated indirectly from their protein content using the Bradford assay, which is an alternative to a direct carbohydrate assay. The system developed was tested by assaying for chondroitin sulfate proteoglycans in sera from patients with various cancers and comparing the results to those obtained for sera from healthy people. The results indicated that this approach could be used as a cost-effective alternative system for determining the amount of these specific biomarker proteoglycans. The column could be reused at least 90 times, with each run consisting of 200 microL of serum sample diluted twofold; an analysis rate of 30 min per run was achieved, as compared to 4 h for a batch procedure.