Andrea Palladio's Renaissance villas are amongst the most famous and widely studied examples of domestic architecture ever produced. The majority of past research about Palladio's architecture employed historical, mathematical and computational methods to analyse their complex proportional systems and rules. In contrast, this paper examines three of Palladio's arguments about his villas plans which relate to their spatial properties and topological connections. Specifically, this paper uses a computational method – the justified plan graph (JPG) – to test two arguments about the location and significance of the primary salon on the plan, and a third about the extent to which the rooms in Palladio's plans are, as he claims, flexible enough to contain alternative functions. Using ten of Palladio's piano nobile (main floor) plans from I Quattro Libri Dell'Architettura as cases, this paper develops mathematical data to test three hypotheses framed around Palladio's plans and theories.