This study focuses on university—industry—government (UIG) linkages and their influence on innovation in Taiwan. The innovation effects are estimated using a quartet of measures — technology transfers, technology licensing, firms incubated and patents granted — while the UIG influence is estimated via its differential impact according to the size of the firms involved, the type of innovation (process or product-oriented), the stage of the technology cycle, and the role of government. Using a Structural Equation Model (SEM) method to examine these interactions, the study reveals that UIG linkage effects vary with the size of company, in that the major incentive for UIG linkages for large companies is an attempt to acquire a skilled and qualified workforce, while SMEs (small and medium enterprises) tend to use them to gain marketing advantage, particularly for those SMEs or start-ups in emerging industries. The study concludes that Taiwan's innovation capacity is heavily reliant on building the capability of SMEs and continues to depend greatly on government leadership through technology-capability-enhancing institutions such as ITRI.