Italy has adopted the strategy of inner areas, mainly based on physical distance from public services. The strategy promotes a multi-level and multi-fund governance approach and the local partnership of mayors. Our paper focuses on rural areas, identified by the national strategy of inner areas, as peripheral and ultra-peripheral, in the Italian insular region (Sicily and Sardinia). It analyzes, at the municipality level, socio-demographic, economic, and environmental sustainability using appropriate indicators. Aiming at discovering the underlying relationship portrayed by multi-attribute data in an information system, we applied rough set theory. The inductive decision rules obtained through this data mining methodology reveal the simultaneous presence or absence of important characteristics aiming at reaching different levels of sustainability. Without the requirement of statistical assumptions regarding data distribution or structures for collecting data, such as functions or equations, this method ensures the description of patterns exhibited by data. Of particular interest is the assessment of conditional attributes (i.e., the selected indicators), and the information connecting them to sustainability, as a decision attribute. The most important result is rule generation, specifically, decision rules that are able to suggest tools for policy makers at different levels.