Environmental factors, different ages, and detection methods might affect the profiles of allergy sensitization and confound the diagnosis of allergic diseases. The purpose of this study was to investigate the different profiles of allergen sensitization in different ages, geographic areas, and detection methods.We analyzed the patients who received allergen sensitization tests by the automated microfluidic-based immunoassay system (BioIC) method at Show Chwan Memorial Hospital in Changhua City and at Chang Bing Show Chwan Hospital in Lu-gang from January 2011 to December 2011. Results were compared in different ages (3-6, 7-18, and ≥19), different geographic areas, and different detection methods and analyzed by Chi-square or Fisher exact test depending on sample size.A total of 1145 patients were analyzed. The younger the age, the higher the food allergy sensitization rate is found (26.6% vs. 14.7% vs.11.1% p < 0.001). The older the age, the higher the sensitization of Blomia tropicalis occurs (33.4% vs.15.1% p < 0.001). The food allergen specific IgE directed against egg white was higher in coast area than city (15.4% vs. 3%, p = 0.015). A higher rate of pollen sensitization was found in the detection by BioIC method (Bermuda grass, 17.2%; Timothy, 12.3%; ragweed, 5.7%). The sensitization rates of cockroach and cat dander were lower in both city and coast areas.Children have higher food allergy sensitization and adults have higher Blomia tropicalis sensitization. Children living in Changhua area no matter in city or coast area had a higher pollen sensitization rate but lower cat or dog dander sensitization rate. Apparently, age, environmental factors, and different methods significantly affect the allergen sensitization in the different areas of Taiwan.