The relative environmental impact from the building construction phase is increasing compared to the operation phase for new buildings. Therefore, it is important to consider the complete environmental life cycle of energy improvement measures. Many advanced optimization methods have been developed in recent years to assess building life cycle impact. However, these previous studies have not fully addressed the secondary effects, in other words, indirect effects outside the actual design option. This may lead to conclusions of optimization studies based on misleading calculation results. The main purpose this study was to highlight the relevance of including secondary effects in optimization of building design with respect to global warming potential and cost. This was done by conducting a parameter study of the building envelope insulation thickness with regard to global warming potential and life cycle costs, while considering secondary effects induced by the different design options. Findings from this study show that secondary effects influence the system boundary, algorithm architecture, results and the final conclusions of optimal building design. Omitting secondary effects can thus lead to incorrect decision on optimal solutions with regard to global warming potential and life cycle cost. Therefore, it is therefore important to take them into consideration when performing optimization studies of building design options.