Keloid disease (KD) is a common fibroproliferative disorder that can occur following cutaneous injury in genetically susceptible individuals. Familial predisposition, high prevalence in certain populations and occurrence in twins suggest a strong genetic component to KD. However, to date no single causative gene has been identified. Copy number variations (CNVs) in genes have been associated with several human diseases including common skin disorders. The objective of this study was, therefore to determine if CNVs in the human genome may contribute to the development of KD. Agilent SurePrint G3 one Million microarrays were used to detect DNA copy number differences in keloid scars of four Caucasian females and compared to commercial reference DNA samples. Subsequent validation was performed with quantitative polymerase chain reactions (qPCR) using 15 KD cases and 27 Caucasian controls. Further validation using a second cohort was carried out with an additional 11 Caucasian controls and 10 KD cases developed from minor skin puncture wounds (caused by acne, vaccination or chickenpox). HLA-DRB1*15 was typed using allele-specific primers in PCR. Five CNV regions located at chromosome (chr) 6p21.32, chr11q11, chr17q12, chr8p23.1, chr22q13.1, chr19p13.1 and chr2q14.3 were selected for validation with qPCR. When comparing controls to subgroups of KD, according to their cause of scarring, chr6p21.32 (primer design targetting HLA-DRB5) was significantly (P < 0.005) associated with KD developed from minor skin puncture wounds, which is further validated using a larger sample size (P < 0.001). The presence of HLA-DRB5 was associated with HLA-DRB1*15 status; 18 out of 19 individuals were positive for both HLA-DRB5 and HLA-DRB1*15 allele. In conclusion, these preliminary findings further support the possible contribution of the HLA genes in KD pathogenesis.