Fanconi anaemia (FA) is an autosomal recessive chromosomal instability disorder with extensive genetic heterogeneity. We determined the genetic subtypes in 28 ethnically and clinically unselected FA patients from Germany and The Netherlands, by complementation analysis. All five currently known complementation analysis. All five currently known complementation groups (FA-A to FA-E) appeared to be represented in the sample studied. The distribution of subtypes differed markedly in the two countries: FA-A patients were most prevalent in Germany (13/22, 59%), whereas in The Netherlands, the majority of patients were FA-C (4/6, 67%). This geographical inhomogeneity has implications for mutation-screening strategies in European FA patients.