In Brazil, as in many other countries, there is no official data on trade flows between subnational regions. Therefore, the estimation of inter-regional input-output systems, under conditions of limited information, has been the subject of researchers at the University of São Paulo Regional and Urban Economics Lab - NEREUS for over two decades. During this span, they have developed two distinctive estimation methods: Supply and Use Interregional Tables (SUIT) and Interregional Input-Output Adjustment Systems (IIOAS). This paper aims to provide a comprehensive overview of these two methods, which were employed to estimate an interregional system encompassing the 27 states within the Brazilian economy. Following the exposition of SUIT and IIOAS methods, a comparative analysis is conducted to delineate their main similarities and differences, in both holistic and partitive terms. The findings underscore that, despite notable differences, particularly in partitive terms, the choice between these two methods generally does not compromise the overall results of structural input-output analysis. Furthermore, this study represents a contribution to the literature, as both SUIT and IIOAS can be applied in the estimation of interregional input-output systems for any country that discloses its Supply and Use Tables and possesses some subnational information for regionalization.