The discovery that lymphotoxin α (LTα) knockout mice lack peripheral lymphoid tissues reformed the study of organogenesis of peripheral lymphoid tissues from a research field that was solely descriptive and dependent on histological methods to one requiring all modern technologies. The concepts of inducer cells for organogenesis of peripheral lymphoid tissues as a separate hematopoietic lineage and of mesenchymal organizer cells have been established through this progress. These discoveries led to the comprehension of the basic framework of the events during organogenesis of peripheral lymphoid tissues. However, many important questions remain unanswered. This review discusses those questions which have arisen from our studies on the organogenesis of Peyer's patches.