The human genome is rich in genomic regions that are repeated several times. These regions are known as CNVs (copy number variations) and can be polymorphic. Moreover, the number of copies may play a role in the predisposition to particular diseases. It is therefore important to accurately determine the copy number of those CNVs in individuals. We have developed a strategy, using concatemeric constructs containing different numbers of repeats as internal standards, to accurately determine the number of repeats in the alpha-defensin and beta-defensin region on chromosome 8p23 by real-time PCR. The test was validated by FISH in DNA of 13 individuals. Comparison with previously published methods shows that this approach provides more accurate results for the determination of the exact number of repeats when they exceed 3 copies. This strategy can be easily transferred to any CNV. With this method we structurally analyzed the alpha- and beta-defensin region in 334 Belgian individuals.