We consider an information system where its throughput deteriorates due to security threats and evaluate information security investment portfolios. We assume that organizations adopt information security countermeasures (or portfolios consisted of countermeasures) to lessen the damage resulted from the productivity (or throughput) deterioration. A probability model is used to derive the system throughput and the average number of repairs according to the occurrence rate of security threats. Considering the revenue from throughput, the repair cost, and the investment for the security system, the net present value for each portfolio is derived. Organizations can compare information security investment portfolios and select the optimal portfolio.