A method for analysing in vitro D4Z4 tandem repeat arrays contained on nucleic acid representative of chromosomes, comprising or consisting of the following steps: a) providing a support on which a nucleic acid sample comprising nucleic acid representative of chromosomes has been previously stretched in linear and parallel strands and hybridizing said nucleic acid with a mix of at least the following probes: - one or several probe(s) called "repeat probe(s)", which is (are) specific for D4Z4 repeat arrays; - one or several probes which enable(s) to distinguish chromosome 4 from chromosome 10; and - one or several probe(s) which enable(s) to distinguish the qA haplotype from the qB haplotype of chromosome 4, wherein said probes are preferably labelled, either all the probes being labelled with the same label(s) or at least one probe, for example at least one repeat probe, being labelled with one or several label(s) different from the label(s) of other probes, and wherein at least one of the probes which enable to distinguish chromosome 4 from chromosome 10 hybridizes with: - a region of the long arm of chromosome 4 which is located at least 45 kb upstream of the centromeric end of the D4Z4 repeat array; or - a region of the long arm of chromosome 10 which is located at least 42 kb upstream of the centromeric end of the D4Z4 repeat array; b) detecting the hybridization signals corresponding to the probes; and c) analysing organization of D4Z4 repeat arrays on nucleic acid representative of chromosomes, in particular: - determining the number of D4Z4 repeat units in said D4Z4 repeat arrays, and/or - determining the orientation of the D4Z4 repeat units in said D4Z4 repeat arrays; and/or - detecting and/or analysing rearrangements in said D4Z4 repeat arrays. a) providing a support on which a nucleic acid sample comprising nucleic acid representative of chromosomes has been previously stretched in linear and parallel strands and hybridizing said nucleic acid with a mix of at least the following probes: - one or several probe(s) called "repeat probe(s)", which is (are) specific for D4Z4 repeat arrays; - one or several probes which enable(s) to distinguish chromosome 4 from chromosome 10; and - one or several probe(s) which enable(s) to distinguish the qA haplotype from the qB haplotype of chromosome 4, wherein said probes are preferably labelled, either all the probes being labelled with the same label(s) or at least one probe, for example at least one repeat probe, being labelled with one or several label(s) different from the label(s) of other probes, and wherein at least one of the probes which enable to distinguish chromosome 4 from chromosome 10 hybridizes with: - a region of the long arm of chromosome 4 which is located at least 45 kb upstream of the centromeric end of the D4Z4 repeat array; or - a region of the long arm of chromosome 10 which is located at least 42 kb upstream of the centromeric end of the D4Z4 repeat array; - one or several probe(s) called "repeat probe(s)", which is (are) specific for D4Z4 repeat arrays; - one or several probes which enable(s) to distinguish chromosome 4 from chromosome 10; and - one or several probe(s) which enable(s) to distinguish the qA haplotype from the qB haplotype of chromosome 4, - a region of the long arm of chromosome 4 which is located at least 45 kb upstream of the centromeric end of the D4Z4 repeat array; or - a region of the long arm of chromosome 10 which is located at least 42 kb upstream of the centromeric end of the D4Z4 repeat array; b) detecting the hybridization signals corresponding to the probes; and c) analysing organization of D4Z4 repeat arrays on nucleic acid representative of chromosomes, in particular: - determining the number of D4Z4 repeat units in said D4Z4 repeat arrays, and/or - determining the orientation of the D4Z4 repeat units in said D4Z4 repeat arrays; and/or - detecting and/or analysing rearrangements in said D4Z4 repeat arrays. - determining the number of D4Z4 repeat units in said D4Z4 repeat arrays, and/or - determining the orientation of the D4Z4 repeat units in said D4Z4 repeat arrays; and/or - detecting and/or analysing rearrangements in said D4Z4 repeat arrays.