In vitro allergen-specific immunoglobulin E (sIgE) measurement has been used as an important diagnostic tool for allergic diseases. Currently, quantitative sIgE levels are detected mainly by using ImmunoCAP and Immulite 2000 assay system. These two systems have the same calibration scale at 0-100 kUA/L, but they differ in used allergens, detection methods and automation systems. We compared 1600 paired sIgE results for 204 allergic patients, including 100 paired sIgE assay results for each of 16 allergens (Alternaria alternata, birch-alder mix, cat dander, D. farinae, D. pteronyssinus, dog dander, buckwheat, crab, egg white, mackerel, milk, peach, peanut, shrimp, soybean and wheat flour). Inter-method comparison was performed for qualitative data with a cutoff of 0.35 kUA/L and a detection limit of 0.1 kUA/L, semi-quantitative class results and quantitative data. In qualitative comparisons, the overall concordance rate ranged from 81.0% to 99.0% (k: 0.599-0.949) with the cutoff value of 0.35 kUA/L. It also ranged from 80.0% to 99.0% (k: 0.521-0.951) with the detection limit of 0.1 kUA/L. The class results from these two assays showed good agreements for all allergens. For quantitative sIgE results, these two assays showed moderate positive correlations for Dog dander (r = 0.683) and Mackerel (r = 0.573) but high to very high correlations for the other 14 allergens (r = 0.734-0.972). Immulite 2000 and ImmunoCAP assays demonstrated good concordance and correlation for 16 common allergens, but international standards against each specific allergen for calibration and harmonization of sIgE tests are still needed.