Alpha defensins are anti-microbial peptides of the innate immune system. The defensin A1 and A3 genes are located in a repeat array of variable copy number (the DEFA1A3 locus) and encode the human neutrophil peptides 1, 2 and 3. The possibility that copy number variation (CNV) may be associated with infection susceptibility and autoimmune pathology motivated the study of DEFA1A3 CNV across populations. We enhanced two existing methods (one qPCR-based and one sequencing-based) to enable copy number estimation that discriminates between DEFA1 and DEFA3 genes. We used these methods to quantify A1/A3 copy number variation in 2504 samples from the 1000 Genomes high-coverage dataset as well as performing FiberFISH assays on selected samples to visualize the haplotypes. These methods produce accurate estimates and show that there are substantial differences between populations. The African population is a clear outlier with a high frequency of the ancestral pure DEFA1 haplotype, but also harbours exceptionally long haplotypes of 24 copies of both DEFA1 and DEFA3, whilst the East Asian population displays the highest mean level of DEFA3 copy number. Further, our findings demonstrate that qPCR can be an accurate method for CNV estimation and that defensins substantially extend the known range of copy number variation for a human protein-coding gene.