OBJECTIVES: According to the Principles on Drug Reimbursement Price Approval(PDRPA) issued by the Bureau of National Health Insurance (BNHI) Taiwan, in the submission of new drug application to Pharmaceutical Benefit Scheme, MTC analyse of several clinical trials could be used to assess comparative effectiveness of the new drug to the currently best treatment(s), with or without the studies directly compared the treatments. Quality of the MTC analysis should be evaluated in a structured way in order to digest the potentially complex analysis. METHODS: We identify the critical points that would have impact on the validity and consistency of the MTC analysis by reviewing the published papers of methodology of indirect comparison of clinical trials. RESULTS: The following checking points were proposed: 1) Check the analysis aim and quality of systematic review, including: topic (patient, intervention, comparator, outcome, PICO), systematic searching for completeness of all relevant studies included, and quality of included studies and extracted data; 2) Check the analysis method and the included materials, including: the framework of comparison; statistical method; identify in each pair of comparison the number of trials included; the important characteristics of each pair of comparison; and meta-analysis result of each comparison pair including the synthesized effect and heterogeneity; and 3) Check the analysis results, including: reanalyze the data with the proposed model; check the consistency between indirect evidence and direct evidence if available; check the sensitivity by constructing the comparison framework from simple (limited comparisons) to complex (all comparisons) or including additional study characteristics; check the results using different statistical models and different effect measurements (such as risk ratio, risk difference, odds ratio etc.). CONCLUSIONS: MTC is a relatively new but potentially valuable method to analyze evidence for comparing effectiveness of several interventions. Experience of using the structural checking points will be built up.