Aeroallergens include dust, pollens, cotton and threshing dust particles. Prevalence of different allergic diseases in Pakistan is about 66.1% and every year, almost 2.4 million people get vaccine for allergy from Allergy Centre, National Institute of Health (NIH), Islamabad. Human Leukocyte Antigens (HLA) genes are located on the short arm of the chromosome number 6 and position 21 and the allele frequency is associated with allergy. The study was conducted to investigate the relationship between the aero-allergens and the frequency of HLA-DRB1*11 and HLA-DRB1*12 allele in aeroallergen sensitized individuals. Blood samples of aeroallergen sensitized individuals were collected at the Allergy Centre, NIH, Islamabad. Then samples were analysed at the Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore during the study period expanded from August 2014 to February 2015 for the presence of HLA-DRB1*11 and HLA-DRB1*12 allele using polymerase chain reaction (PCR). While total level of Immunoglobulin E (IgE) was measured by enzyme linked immunosorbent assay (ELISA) in all serum samples. This study indicated that the frequency of both alleles HLA-DRB1*11and HLA-DRB1*12 in aero allergy patients is less as compared to healthy controls. HLA-DRB1*11 demonstrated significant association with aeroallergens and could have a protective role for allergy while HLA-DRB1*12 did not show any association with aeroallergen sensitization.