Nijmegen breakage syndrome (NBS), a rare autosomal recessive chromosomal instability disorder, is caused by mutations in the NBN gene. Most patients known so far are of Slavic origin and carry the major founder mutation c.657-661del5. Due to an unexpectedly high incidence of NBS patients (homozygous for the c.657-661del5 mutation) in a Northeast Bavarian region in Southeast Germany, we estimated the prevalence of this mutation in this area and compared it to another German region. We found a high carrier frequency of 1/176 for the c.657-661del5 mutation among newborns in Northeast Bavaria, while the frequency of the mutation in Berlin was 1/990. We further studied families from a Slavic population isolate, the Sorbs, in the Lusatian region in Northeast Saxony, and revealed a prevalence of the c.657-661del5 mutation of 1/34. Whereas the Slavic origin of the Sorbs has been known, we attribute the surprisingly high frequencies of c.657-661del5 mutation in Bavaria (similar to frequencies of this mutation in various Eastern European countries) to a high percentage of people of Slavic origin in Northeast Bavaria.