In a previous hemochromatosis screening study including a total of 65,238 individuals, 566 persons were genotyped for the C282Y and the H63D mutations. Of these, a total of 433 samples (298 homozygous C282Y and 135 homozygous wild type) were reanalyzed to investigate if the potential presence of the newly described 5569G/A polymorphism had confounded the genotyping results for the C282Y mutation. Genotyping with a polymorphism-insensitive primer pair yielded no samples that altered their genotype. By utilizing the polymorphism-sensitive primer pair and elevated annealing temperatures, 133 samples previously genotyped as heterozygous C282Y were reanalyzed to verify the presence of the polymorphism in the population studied. Out of a total of 266 chromosomes, we found the polymorphism present in 9 chromosomes, yielding an allele frequency of 0.034 in this particular subpopulation. In one of the samples, the polymorphism was present on the same DNA strand as the C282Y mutation. We conclude that in the population studied, the 5569 G/A polymorphism is present, but its presence had no implications for the outcome of the previous genotyping. Nevertheless, we recommend that C282Y genotyping by restriction endonuclease digestion of PCR products in the future should utilize a primer pair that is not influenced by the 5569G/A polymorphism.