Uganda, like many other African countries has not been developing primary science, technology and innovation Indicators and to make them accessible to public and private sector decision makers for social economic development and investment purposes. Indicators have not been given serious attention as engines of long-term development. This paper reports the results of a research undertaken to develop a set of relevant science, technology and innovation Indicators for Uganda. From a population of 7,336 firms, 300 firms were sampled for innovation surveys and 200 institutions for the Research and Development survey. The data collected were represented in tables and was grossed up. Data entry was taken in CSPRO and the analysis was done using STATA statistical software There is a global perception that businesses in developing countries like Uganda are generally dominated by Small and Medium enterprises; and that is where most innovations were happening. This paper will discuss the core indicators of Research and Development (R&D) and Innovation; the empirical data of the state of Uganda’s Science, Technology and Innovation Indicators. The paper further explores the potential benefits and the best practices in incubation process. The major conclusions are; prioritizing science and technology policy will create more opportunities and build capabilities for innovations and technology. The monitoring of industry, government and university R&D programs is crucial to successful policy making and analysis.