Dear Editor, We would like to add some new results to our recent publication about Alu repeat-induced autosomal recessive chronic granulomatous disease (CGD) [1]. CGD patients are susceptible to severe infections with certain opportunistic bacteria and fungi and also often suffer from granulomatous inflammation even in the absence of infection. The disorder is caused by genetically determined defects in components of the phagocyte multienzyme complex NADPH oxidase. Recently, we characterized several patients with autosomal recessive p67-phox-deficient CGD evoked by an Alu repeat-induced deletion within the NCF2 gene [1]. The NCF1 gene encoding p47-phox also contains several Alu repeats that may contribute to recombination events with one of the two highly homologous unprocessed NCF1 pseudogenes, thereby causing p47-phox-deficient CGD [2, 3]. In this letter, we show for the first time that autosomal recessive p47-phox-deficient CGD can also be caused by an Alu repeat-induced deletion within the NCF1 gene. We found two CGD patients of different families with the same mutation c.154−283_451+821del2858 in NCF1 [4] and, thus, a deletion of exons 3–5 in their p47-phox cDNA. In one of the patients, this deletion was present in homozygous form; in the other, in heterozygous form together with a complete NCF1 deletion. The two families are most likely unrelated, and only one of the patients has consanguineous parents. One family is of Polish, and the other is of German origin. Furthermore, a short tandem repeat (STR, hg19_chr7, 7201262–7201312) located 2 Mb from the NCF1 gene has nine repeats in one and ten repeats in the other family, and an STR close to the NCF1 gene (hg19_chr7, 73943032–73943364) differs by one repeat on the allele with the complete deletion of NCF1 and by two repeats on the allele with the deletion of exons 3–5 between the two families (data not shown). Surprisingly, we nevertheless found exactly the same genomic sequence in both patients (Fig. 1, marked in gray). The Alu repeat located downstream of exon 2 crosses over to the Alu repeat upstream of exon 6, thereby deleting the 2,858-bp DNA stretch comprising exons 3–5. The putative crossover region is marked in dark gray, and possible gene conversions are indicated by bold arrows. Such gene conversions are frequently associated with Alu-repeat induced crossovers (see also figure legend). Specific analysis of the cDNA with the three-exon deletion (thus avoiding pseudogene cDNA) revealed that all SNPs in exonic regions [2] were of NCF1 wild type and not of pseudogene origin (data not shown). Therefore, we found no hint of a crossover of the wild type with one of the NCF1 pseudogenes, even though we cannot completely rule out this possibility. In conclusion, Alu repeats can cause deletions not only in the NCF2 but also in the NCF1 gene, resulting in autosomal recessive CGD in both instances. Breakpoints and gene conversion hot spots within the Alu repeats of these genes Stefan Winkler, Karin van Leeuwen, Dirk Roos, and Joachim Roesler contributed equally.