The integral basic component of any state economy is the energy sector; alongside with this energy security plays an important role in a national security guarantee. Natural gas supply disruptions would disturb as industrial, as household sector, therefore precise security level assessment of natural gas supply system becomes more acute. The target of the Doctoral Thesis is to elaborate the security assessment methodology of natural gas supply system. Estimation of security of energy supply concept argues absence of joint understanding and any approach of explanation of this concept, thus the definition of security of natural gas supply has been formulated in this Doctoral Thesis. The results of the analysis reveal that security of natural gas supply is defined with differing concept-based techniques and various indicators, yet being not interrelated, which specifies the lack of the uniform methodology. According to the definition formulated in the Doctoral Thesis, as well as to the principles of the theory of constraints, N-1 infrastructure standard was identified as the minimum security indicator of natural gas supply system. Based on the Doctoral Thesis elaborated allocation of natural gas flows in the common Baltic natural gas supply system for the cases of natural gas supply disruptions, it was concluded that N-1 infrastructure standard had significant shortcomings. Furthermore, the necessary amendments to the calculation formula for N-1 infrastructure standard were stipulated. The minimum security assessment methodology of natural gas supply system was stipulated in the Doctoral Thesis, and is used to define the sufficiency of natural gas supply infrastructure in cases of natural gas supply disruptions, preventing the possible negative impact to consumers. The methodology is elastic, easy adaptable and applicable for all the countries regardless the scale of their natural gas supply system, it is also applicable for other sectors of energy industries, specifically, for power or heat supply. The elaborated and verified the minimum security assessment methodology of natural gas supply system will allow to estimate sufficiency of natural gas supply infrastructure in cases of natural gas supply disruptions and will provide fast decision making on alternative sources of natural gas or necessary co-operation in organizing natural gas flows, thus reducing the disruption risks of natural gas supply. The Results of the Doctoral Thesis have been reported at 14 international conferences and reflected in 8 publications.