Multiplex SNP discrimination in the multiple codons of the genomic DNA is demonstrated by applying controller DNA technology (CDT) to MDR-TB 9G DNAChips. CDT allowed the efficient detection of 20 SNPs in five codons of the genomic DNA in 40 min. CDT could distinguish SNP targets to as low as 1 copy of the genomic DNA. 100% agreement with the sequencing analysis of clinical samples highlighted the clinical applicability of MDR-TB 9G DNAChips.