Background: Viet Nam, the 12th highest TB burden country in the world, has not shown significant decrease in TB incidence rate over the past years, despite its model National TB Control Program (NTP) and its attainment of the global target since 1997. One of the possible explanations for this is the mathematical model used to capture the dynamics of TB epidemiology might be insufficient (e.g., the emergence of the more virulent strains Mycobacterium tuberculosis (M. tb) Beijing genotype, drug resistance, HIV co-infection in young adults, the negligence of the strong influence of diagnostic delay, risk factors associated with demography. This study therefore aimed to further investigate the hypothesis that Viet Nam s TB epidemic can be explained by molecular characterizations, drug susceptibility patterns and their association with demographic factors.Methods: 580 M. tb strains collected in 5 TB hospitals from 3 main regions of Viet Nam during 2009-2010 and 100 historic strains isolated during 1996-2008 were analyzed by Spoligotyping and identified genotype. Then, 252 Beijing strains assigned by Spoligotyping were further analyzed by IS6110-RFLP. The discriminatory of RFLP patterns was compared using BioNumerics software. The information from participants collected through questionnaires was statistically analyzed by SPSS software.Results: M. tb population in Viet Nam was comprised of 19 different genotype families that assigned to 11 pooled families by Spoligotyping results. Beijing and East-African-Indian (EAI) were the most prevalent. Among 580 newly collected strains, 44.7% were Beijing genotype. This genotype was more prevalent among patients who had drug resistance, lived in urban area, of young age and are female. 238/252 of the Beijing strains were belonged to one group with high similarity of IS6110-RFLP patterns but not identical. 7/22 multi-drug resistance (MDR)-TB Beijing strains were identical to non-MDR-TB strains. The strain patterns from the North were diverse while that from the South were disseminated. The atypical Beijing RFLP patterns with low-copy of IS6110 was found in 6/252 (2.4%) strainsConclusion: The Beijing genotype has been predominating in the nation since 1996. However, its prevalence is declining from 54% in the 1998-1999 study to 44.7% in our study, while EAI family seems to be expanding. In Viet Nam, Beijing genotype is associated with patients who have urban residence, younger age, female gender, drug resistance but not with BCG vaccination history. One third of the MDR-TB strains were identical to non-MDR-TB strains demonstrating that MDR-TB had been acquired after transmission. The atypical Beijing patterns with low-copy of IS6110 is tended to be eliminated from the M. tb population. The differences between the IS6110-RFLP strain patterns of the North and the South suggested that the M. tb Beijing populations of the two regions were possibly derived from different ancestor strains.