A comprehensive seismic risk assessment has been performed for the existing route of the 3rd Azerbaijan natural gas buried pipeline in Iran. The major active seismic sources along the pipeline were identified and the geometrical parameters as well as the seismicity rates were determined. The seismic hazard assessment of the ground vibrations along the pipeline was performed in the framework of the Probabilistic Seismic Hazard Analysis using the CRISIS 2007 software. All of the components of the gas pipeline along the route were identified and the corresponding fragility functions are established through the methodology described in the HAZUS guideline. A detailed cost analyses was taken into consideration based on the expert opinions in the National Iranian Gas Company, in order to provide more practical loss model for the pipeline route. Also, a simple method is suggested in order to account for the vent gas in the total loss estimation. The spatial analysis of the hazard function layer in combination with the loss model layer, in Geographical Information System platform, reveal the financial consequences of different earthquake scenarios.