The paper discusses the similarities and the incompatibilities between two forms of Energy Analysis (exergy and emergy, 'EXA' and 'EMA' in the following), both of which try to represent the behavior of physical systems by means of cumulative energy input/output methods that result in a double integration over space and. time domains. Theoretical background, definitions and balance algebra are discussed first, in a 'statement-counterstatement' format that helps pinpointing differences and similarities. A significant, albeit simplified, benchmark case (ethanol production from corn) is used to compare the results and analytically assess the merits of each approach as well as possible synergic aspects. Corn production, transport and industrial conversion to ethanol are included in the analysis. First, mass balance and energy accounting are performed in each step of the process, then, exergy and emergy evaluations are carried out separately to lead to a set of performance indicators, the meaning of which is discussed with reference to their proper scale of application. The Authors underline that each method has its own preferred field of application and conclude that the two approaches appear to be characterized not much as different (and therefore 'competing) tools, but as different paradigms, whose meta-levels (their 'philosophies') substantially differ. In particular, EXA is found to provide the most correct and insightful assessment of thermodynamic features of any process and to offer a clear quantitative indication of both the irreversibilities and the degree of matching between the used resources and the end-use material or energy flows. EXA combined with costing considerations results in Thermo-Economics (TE), presently the best engineering method for System optimization. One of EXA recent extensions, Extended Exergy Accounting (EEA) includes all externalities in the exergy resource accounting, thus providing a more complete picture of how a process is interacting with its socio-economical environment and with the Biosphere. EMA further expands the evaluation to the larger scale of the Biosphere and properly accounts for the globality of the energy and resource flows supporting complex living systems. Although some conceptual assumptions and methodological differences appear irreconcilable, important similarities are also found that may lead to further methodological and practical convergences. Note: Although a significant confrontation and debate accompanied the development of this paper, contrasting opinions about important features of the two approaches still exist. Therefore, SU takes full responsibility of statements in Sections 2,4.1, 6.2, 7.1 while ES takes full responsibility of statements in Sections 3,4.2, 6.1, 7.2. All remaining Sections reflect points of view agreed upon by both Authors. © 2004 Elsevier Ltd. All rights reserved.