Abstract: This paper examines conceptual issues and reviews empirical results bearing on the relationship between research approaches emphasizing organizational capabilities and those based in transaction cost economics (TCE)—or in organizational economics more generally. Following a review of conceptual fundamentals—what capability is and why organizations differ in capability—it assesses recent progress toward an integration of the capabilities and transaction cost approaches, primarily in the context of the analysis of vertical structure and related phenomena. This review suggests that progress has been substantial and that the key elements of a promising dynamic synthesis have been identified. The paper then considers issues that call for attention if further progress is to be achieved. The first of these is the role of agency, which must be seen in expansive terms (relative to standard economic rationality) if its evolutionary significance is to be fully appreciated. The second is the role of structure, or more specifically, industry architecture, which affects capability development by way of its effect on the feedback that firms receive. After drawing on the recent financial crisis for an illustration of these ideas, this paper considers the rise of interest in business models as a useful field of application, and it concludes with a discussion of the role of organizational economics (beyond TCE). We argue that, whatever the theoretical perspective at the level of the firm, analyses must reach beyond that level to grasp the important causal forces affecting capability development, firm boundaries, and structural features more generally.