Background: Virulence factors as well as host immune response play an important role in disease susceptibility. There are no known studies associating the presence of HLA class I and II alleles with the CHIKV infection in Latin America. We aim to identify Human Leukocyte Antigen (HLA) alleles present in patients with the chikungunya virus (CHIKV) infection when compared to healthy controls, as well as their association with the clinical spectrum of the disease. Methods: We carried out a cross-sectional analysis nested in a community cohort. We included patients 18 years and older with serological confirmation of CHIKV infection. We performed HLA typing of HLA-A, HLA-B and HLA-DRB1 alleles. We used two-by-two tables to establish associations between allele presence and clinical characteristics. Findings: Data from 65 patients with confirmed CHIKV infection were analysed for HLA typing. CHIKV infection was associated with the presence of HLA-A*68, HLA-B*35, HLA-DRB*01, HLA-DRB1*04 and HLA-DRB1*13 alleles. Rash in the face or the abdomen was associated with the presence of HLA-DRB1*04. Interpretation: Our study demonstrated that in our cohort, HLA type I and type II alleles are associated with CHIKV infection, and specifically an HLA type II allele with dermatological symptoms. Our results suggest the need of further research and set a path for future investigation on genes outside the HLA system to help elucidate the pathophysiology of the CHIKV infection as well as its interaction with its host. Funding Statement: The study was supported by the Colombian Rheumatology Association (ASOREUMA) under grant number Acta 169 10th July 2015; Universidad de La Sabana under grant number MED197-2015; and COLCIENCIAS doctoral scholarship under grant number 757-2016.Declaration of Interests: The authors declare no conflict of interest.Ethics Approval Statement: Informed consent was obtained, prior to the patients' admission. The study was approved by the ethics committee from La Universidad de La Sabana (study approval MED-197-2015) and the Hospital Militar Central (study approval 106-2016).