In the last 20 years, state governments have funded a large number of science-based economic development programs. Remarkably, there have been few evaluations of either their economic impact or their prospects for economic impact. The 2004 decision by California voters to issue bonds to fund $3 billion of research on human pluripotent stem cells is an ideal case study for introducing an evaluation methodology for the progress by state programs in developing and transferring research results. In the process of evaluating the California stem cell initiative, we make three methodological contributions to the study of the impacts of sub-national science-based economic development programs. First, the following data sources are introduced as indicators of the prospective economic benefits of these programs: changes in targeted federal research funding, patenting, small business investment research grants, venture capital investment, new firm formations, and clinical trials. Second, the use of regional or industrial controls is introduced. In the case study of the California stem cell initiative the regional control is the comparison of the two dominant California stem cell research and firm clusters, San Diego and the San Francisco Bay Area, to the other dominant cluster, Boston. The biotechnology industry, as a whole, is used to control for exogenous shocks such as changes in the overall interest in new life science technologies. Third, because technology transfer is predicated upon commercialization, a value chain perspective can visualize commercialization obstacles. In this study, a stylized human stem cell therapy value chain is compared to the existing biotechnology value chain and the differences suggest areas where human stem cell therapies are likely to face difficulties. The discussion and conclusion evaluates the progress of the California stem cell initiative and suggests that the evaluation methodology developed can improve the evaluation and guidance of science-based economic development programs.