Japanese archaeology benefits from the large number of rescue excavations conducted during recent decades that have led to an unparalleled record of archaeological sites. That record is here put to use to interrogate changing settlement patterns in the north-eastern corner of Tokyo Bay during several millennia of the Jomon period (Early, Middle and Late Jomon: 7000–3220 cal BP). Jomon hunter-gatherer occupation is characterised by large numbers of settlements, some of them substantial in size, containing hundreds of individual pit-house residential units. Detailed analysis of the rank-size distribution of these settlements reveals a pattern in which periods of settlement clumping, with few large settlements, alternate with more dispersed settlement patterns on a regular cycle of approximately 600 years. The regularity of this cycle might suggest a correlation with cycles of climatic change, such as Bond events. Closer scrutiny shows, however, that such a correlation is unconvincing and suggests that cyclical change in Jomon settlement patterns may instead be due to other factors.