The research describes the issues affecting the Basilica of St. Peter and Paul in Agliate (Italy) and the methods developed for its survey. The Basilica is part of an important medieval complex, the dating of which remains uncertain. The current structure is the result of multiple interventions over time, including extensive restoration work carried out in the final decades of the 19th century. Since the initial inspections, the stone columns of the ancient Basilica have been identified as the most critical structural elements. These columns were constructed using drums taken from earlier Roman-era structures. This has led to significant heterogeneity in the load-bearing columns, with visible discontinuities, cracks, and high misalignments. It was therefore essential to design a survey campaign specifically focused on assessing the extent and significance of the visible damage. This paper outlines the main operational steps of the survey and non-destructive tests. Furthermore, it presents the initial results, which will form the basis for future conservation strategies of the load-bearing structures.