Family medicine is a relatively new and rapidly growing discipline in Japan. Nevertheless, for family medicine to achieve recognition as a unique medical discipline in Japan, family medicine must develop its own research agenda and appropriate research methods. However, existing literature in Japanese for guiding the design of family medicine research is scarce. This paper introduces strategies for identifying research questions that emerge from clinical “stories” and connects them with appropriate research designs. This paper provides examples of major categories of research designs including those using a single method and mixed-methods designs that take advantage of the strengths of both qualitative and quantitative methods. A solid research foundation in family medicine needs to be established that preserves the unique attributes of this generalist discipline. Family medicine researchers are needed who can lead research teams to address the complex research questions emanating from primary care clinical practice.