This study examines the intra-site structure of two Late Mesolithic sites in southeast Lithuania: Gailiūnai 2 and Varėnė 2. Gailiūnai 2 presents a rare example of a single-period camp with a well-preserved spatial structure of discrete lithic scatters. In contrast, Varėnė 2 is a multi-period palimpsest site with mixed archaeological deposits but with documented Mesolithic features. Spatial analysis, characterisation and refitting of lithic artefacts as well as AMS 14C dating were carried out in order to identify the patterns in the internal organisation of both sites and define the nature of activities that resulted in the formation of their particular structure. The analyses have shown that three discrete lithic clusters at Gailiūnai 2 likely reflect remains of short-term task-specific encampments with the western cluster also displaying evidence of a surface dwelling. Refitting revealed prevalence of short reduction sequences and a technological organisation indicative of short-term stays. Varėnė 2 represents repeated, more substantial occupations involving habitation inside dugout dwellings as well as potential reuse of their pits as dumps. While individual lithic scatters are impossible to distinguish, three dugout structures with artefact-rich fills indicate more substantial habitation for longer periods. Radiocarbon dating has shown that dugouts were probably used between ca. 7170 and 4800 cal BC and in separate phases. The Late Mesolithic habitation at Varėnė 2 involved extensive usage of distinctive reddish-banded flint, which was used contemporaneously with the inhabitation and burial at one of the dugouts. The contrasting site structures highlight variability in Late Mesolithic settlement strategies. These results demonstrate the potential of unstratified sandy sites to reveal meaningful insights into lifeways of Stone Age hunter-gatherers in the southeast Baltic.