The development of reliable earthquake mitigation plans and seismic risk management procedures can only be based on the establishment of comprehensive earthquake hazard and loss scenarios. Two cities, Grevena (Greece) and D$ddot{u}$zce (Turkey), were used as case studies in order to apply a comprehensive methodology for the vulnerability and loss assessment of lifelines. The methodology has the following distinctive phases: detailed inventory, identification of the typology of each component and system, evaluation of the probabilistic seismic hazard, geotechnical zonation, ground response analysis and estimation of the spatial distribution of seismic motion for different seismic scenarios, vulnerability analysis of the exposed elements at risk. Estimating adequate earthquake scenarios for different mean return periods, and selecting appropriate vulnerability functions, expected damages of the water and waste water systems in D$ddot{u}$zce and of the roadway network and waste water system of Grevena are estimated and discussed; comparisons with observed earthquake damages are also made in the case of D$ddot{u}$zce, proving the reliability and the efficiency of the proposed methodology. The results of the present study constitute a sound basis for the development of efficient loss scenarios for lifelines and infrastructure facilities in seismic prone areas. The first part of this paper, concerning the estimation of the seismic ground motions, has been utilized in the companion paper by Kappos et al. (2010) in the same journal.