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A polymorphic insertion – deletion in APOBEC3B gene may modulate the activity of the protein by altering the stability of the fusion mRNA, therefore may influence the infection diseases clinical progression. However, data regarding the APOBEC3B insertion – deletion polymorphisms status in the Javanese multi-drug-resistant tuberculosis patients is unknown. This study evaluated the prevalence of APOBEC3B insertion – deletion polymorphisms in Javanese multi-drug-resistant tuberculosis patients. In total, 37 blood samples from 37 Javanese multi-drug-resistant tuberculosis patients in Dr. Moewardi General Hospital Surakarta collected from 2012 until 2015 were subjected for genomic DNA isolation. Genetic polymorphisms of APOBEC3B insertion – deletion were detected with polymerase chain reaction techniques. The genotypes were defined according to generated fragment patterns in the agarose gel electrophoresis analysis of PCR products. APOBEC3B insertion/insertion was detected in 56.8% (21/37) patients. APOBEC3B deletion/insertion was detected in 37.8% (14/37) patients. Two patients had APOBEC3B deletion homozygote. The APOBEC3B insertion homozygote was found predominant in Javanese multi-drug-resistant tuberculosis patients. The polymorphisms found may associated with clinical status of the patients.