Background: Duchenne muscular dystrophy (DMD) is major childhood muscular dystrophy. Pre-implantation genetic testing (PGT) is an alternative to prenatal diagnosis. This study performed SNP microarray with karyomapping PGT of DMD in comparison to PCR-based techniques for validation. Methods: Two families at risk of having DMD offspring decided to have karyomapping PGT. PCR protocol using mini-sequencing and intragenic microsatellites-based linkage analysis was developed and applied. Results: Karyotyping results of family DA (DMD c.895G>T) exhibited three normal, two carriers, two affected and two with intragenic recombination. Karyomapping results of family DB (DMD exon 8 and 9 duplication) showed four normal, two carriers, two affected and one with intragenic recombination. One embryo was chromosome unbalanced and one was uniparental disomy. Conclusion: Successful karyomapping PGT for DMD was successfully performed. Limited number of embryos were tested due to its expensive consumables. Intragenic recombination precluded haplotyping. Karyomapping provides advantages of CNV and parental origin information.