Our aims were to evaluate the performance of an automated microfluidic immunoassay system for measuring allergen-specific IgE (sIgE) in sera against an established in vitro assay and to assess the system's diagnostic accuracy against objective clinical criteria for identifying sensitization to specific allergens in daily practice of allergy clinics. Using both the automated microfluidic-based immunoassay system (BioIC and ImmunoCAP, we measured sIgE in serum samples from 212 children who visited allergic clinics in two medical centers. Outcomes of skin prick tests (SPT) served as the clinical comparison method. The assay results of targeted allergen of BioIC have a good correlation with ImmunoCAP in the diagnosis of allergen sensitivity by patients' clinical history. When comparing the test results of the sIgE against overall allergens, in either two tests among the three assays performed showed high percentage of agreement between BioIC and ImmunoCAP (77.8%, 95% CI: 72-83.3%) but not with SPT (BioIC 64.9%, 95% CI: 58-72%; ImmunoCAP 67.5%, 95% CI: 61-74%). Using ROC analysis and SPT as quasi-standard, BioIC and ImmunoCAP have nearly the same performance of sensitivity and specificity in the confirmation of SPT results. The total and within one-class agreements of each allergen test result between BioIC and ImmunoCAP ranged between 55.2% and 99.5% with an overall average of 80.9%. Laboratory testing for sIgE can be performed on a fully automated, microfluidic cartridge system with advantages of low sample volume, simultaneously tested allergens, and with diagnostic accuracy for representative allergens equivalent to the semi-automated CAP technology.