While systems of systems (SoS) are starting to reach the market, it is not entirely evident how to analyze safety, and on a high level also security, of such systems. In fact, specific characteristics of SoS, such as independence, changing constitution, evolutionary development, and emergent behavior, provide certain challenges to the safety analysis. In this paper, such challenges are summarized and a systems theoretic safety analysis method, abbreviated as STAMP, is evaluated on an automotive SoS application example. In conclusion, STAMP seems well positioned to serve as a base for a future method for safety and, to a certain degree, security analysis of SoS, although some work remains to be done. The advantages and limitations of the STAMP approach when dealing with SoS are discussed.