The historical architectural heritage may be considered as the product of a complex system of interaction between several factors - cultural, socio-economic, technical, aesthetic etc. The restoration and conservation of this important heritage, therefore, requires necessarily a multidisciplinary approach, both in the preliminary phase of knowledge and in the operative one, strictly connected to the first, regarding the development of the restoration works in all their steps, from the project to the realization. The historical-critical analysis of bibliographic, archival and iconographic sources, together with the architectural survey, aims at interpreting all the events that, from the initial project to all the eventual phases of transformation, have lead the monument in its current state. This is therefore a multi-temporal and multi-spatial study in which geomatics gives an innovative contribution for its capability of gathering, storing, processing, and delivering different levels of spatially referenced information. The current techniques of architectural survey, supported by specific methodological skills, are therefore not limited to a mere mathematical-geometrical description of the historical building, but are useful also for many other purposes, such as formal-linguistic analysis, interpretation of the historical phases of transformation, description of the state of degradation/conservation etc. In this interdisciplinary perspective, photogrammetry and laser scanner represent the two main techniques, as they offer the greatest potential of performing integrated surveys. In the last decades, we have witnessed the growth and development of these 3D-survey techniques as alternative or complementary tools to the traditional ones. In particular, in the field of architectural restoration, these techniques have made significant improvements not only in terms of measure precision or reduction of time for survey operations, but also for the possibility to represent and visualize the historical building in its context. These modern techniques of survey, based on the creation of point clouds, are now widely used both in the study of a building and for the thorough description of architectural details and decorations. This paper aims at describing the methodological approach and the results of the 3D survey of the Chapel of St. Agata in Pisa, aimed at its restoration. For the development of a restoration project, the survey drawings must represent not only the geometry of a building, but also the materials and the level of degradation. So, we chose to use both the laser scanner - which guarantees uniformity of the geometric survey precision - and a 3D image-based modelling. The combined use of these two techniques, supported by a total station survey, has produced two point clouds in the same reference system, and allowed the determination of the external orientation parameters of the photographic images. Since these parameters are known, it was possible to texturize the laser scanner model with high quality images. The adopted methodology, as expected, gave back metrically correct and graphically high-quality drawings. The level of detail of the survey, and consequently of the final drawings, has been previously defined for the identification of all the elements required for the analysis of the current state, such as the clear identification and position of all the degradation phenomena, materials and decorative elements such as some fragmented and heavily damaged frescoes.