Killer cell immunoglobulin‐like receptors (KIR) form a group of regulatory molecules that specifically recognise human leukocyte antigen (HLA) class I molecules, modulating the cytolytic activity of natural killer cells. The purpose of this study was to investigate the influence of KIR genes and their class I HLA ligands in susceptibility to dengue fever in a population from southern Brazil through a case–control study. One hundred four subjects with confirmed diagnoses of dengue participated in this study, along with a control group of 172 individuals from the same geographic area. HLA and KIR genotyping was performed by polymerase chain reaction with sequence‐specific oligonucleotide probes (PCR‐SSOP) and with sequence‐specific primer (PCR‐SSP) techniques, respectively. Data analysis showed significant differences for the KIR2DS1 (54.8% vs 40.7%, P = 0.03), KIR2DS5 (50.0% vs 36.0%, P = 0.03) and KIR2DL5 (76.0% vs 56.4%, P = 0.001) genes. With regard to KIR‐ligand pairs, positive associations with dengue were observed in KIR3DS1‐Bw4 (45.2% vs 29.7%, P = 0.01), KIR3DL1‐Bw4 (80.7% vs 65.1%, P < 0.001), KIR2DL1‐C2 (75.0% vs 62.2%, P = 0.03) and KIR2DS1‐C2 (40.4% vs 25.6%, P = 0.01) interactions, and a negative association in KIR2DL3‐C1/C1 (18.2% vs 33.1%, P = 0.01). Furthermore, the analysis of KIR haplogroups showed a possible protective factor against dengue fever in individuals with the AA genotype. Taken together, these results suggest the existence of genetic predisposition to dengue fever in the population from southern Brazil.