Background: Introduction of molecular diagnostic tools revolutionized the management of the multidrug resistance tuberculosis (MDR-TB). Strategies to optimize utilization are needed to reverse the current trend and exceed the achievements attained in TB control. Objectives: To determine the effect of molecular diagnostics in referring patients for MDRTB treatment in terms of duration from diagnosis to start of treatment, and eventually treatment outcomes. Methods: This was a cross sectional hospital based study conducted at Kibong’oto National Tuberculosis Hospital in Tanzania (KNTH). Data were collected from KNTH patients’ hospital charts, MDR-TB program cards and registers using a designed questionnaire. Collected data were reviewed from January 2013 to December 2013and entered into data base where they were analysed according to objectives Results: A total of 95 MDRTB cases were referred for treatment in 2013 at KNTH. Eighty-four (80%) patients were analyzed. Seventy seven (91.7%) were diagnosed by molecular methods. Thirty six cases (43%) were HIV co-infected with 21 (60%) having CD4 count of less than 200cell/mm3. Sixty nine cases (82%) had history of previous TB treatment. The time from specimen collection to treatment initiation was reduced from 7 months by the conventional methods to 22 days by molecular methods. Sixty six cases (80%) were discharged after finishing intensive phase of treatment. Seventy three (90%) achieved culture convention and 67 (92%) converted within 2 months of treatment. Conclusion: The findings consolidate evidence based strategies to optimize MDR-TB diagnosis using molecular diagnostics with the overall goal of halting MDR-TB transmission in the community. Key words: Multi-drug Resistance Tuberculosis, molecular diagnostics, management, Tanzania