A number of the Alu and L1 elements present within the centromeric reg
ions of the human chromosomes have been analyzed by polymerase chain r
eaction amplification. The oligonucleotide primers were homologous to
the 3' end consensus sequences of either Alu or L1 in conjunction with
an oligonucleotide primer homologous to alphoid sequences specific to
different chromosomes. This allowed one to detect an unusual number o
f Alu and L1 polymorphisms at different loci. It is proposed that this
results from molecular rearrangements which occur within the a-satell
ite DNA in which they are embedded (Marcais et al. J. Mol. Evol. 33:42
-48, 1991) and not because the centromeric regions are targets for new
insertions of such elements. The same analyses were made on cosmids a
nd YACs originating from the centromeric region of chromosome 21 as we
ll as on a collection of somatic hybrids containing chromosome 21 cent
romere as unique common human genetic material. The results were consi
stent with the above hypothesis.