The basilica of St. Anthony in Padua (13th-14th cent.) is one of the most remarkable pilgrimage sites in Italy. To date, the monument itself has never been subject to a comprehensive stratigraphic analysis. Important information about the construction sequence of the building may be conserved in the domed roofs protecting the inner masonry shells.The present paper will focus on the dome next to the facade. During the survey, data acquisition via laser scanner have been flanked by standard tasks. Specifically, the stratification analysis of the timber framework of the dome requires to measure the entire structure, including parts with difficult access, and calls for many scan bases to go further the sight obstacles represented by the rafters and the horizontal collar-beams. Therefore, application of laser scanning might appear difficult at first sight. The authors will show that the approach confirms the suitability of the laser scanner technology in facing the general complexity of the structure. The development of a graphic documentation in CAD environment entailed a manageable complexity in terms of time-consumption and precision in data processing. So far, the plans reveal the irregular profile of the dome in its inner masonry shell, and of the outer masonry drum. The sections show a two-centre curvature of the elevation of the outer timber shell. However, the joints among the rafters, ribs, and tie-beams still require a series of traditional in-depth assessments acquired in close-range access. Nevertheless, the pragmatic investigative modus operandi, tested up to now, does represent a fixed protocol suitable to be iterated and perfected for each cupola. In such complex structures, the laser scanning process confirms to be a valid strategy to reach a good compromise between time consumption, human effort, and millimetre precision. In this way, the collected material provides a first contribution to acquire knowledge on this Italian medieval masterpiece, which stands out on the international scenario for its historical richness and architectural complexity.