Houses and burials recorded in the settlements of Lepenski Vir I and II and burials previously ascribed to Lepenski Vir III are here discussed in view of the recent analyses of archaeological material and re-analyses of the field burial record from this site. Evidence of pottery in situ in houses of Lepenski Vir I, together with the evidence for important dietary change in the Lepenski Vir community in the course of the second half of the seventh millennium cal BC, reinforces the assumption, made by a number of scholars over several previous decades, of intensive contacts between early Neolithic groups and local hunter-gatherers. Burial practice throughout the seventh and sixth millennia cal BC at Lepenski Vir is thus reanalyzed in this new light. Apart from burials unrelated to architectural remains, five ‘types’ of burial deposition are noted in relation to houses of Lepenski Vir I–II, all but one having a distinct chronological and spatial patterning. The inhabitants' choice of mode of deposition of the deceased is always associated with a certain location in the settlement, sometimes used over several centuries. In the course of their history, these locations were often used for building a particular house or group of houses. The content of such houses is also discussed wherever it was possible. Duality in settlement organization could also be recognized in the burial practices related to settlement architecture. The attribution of the majority of burial remains to early Neolithic Lepenski Vir III is here also questioned in the light of new data and reinterpreted settlement sequences.