The purpose of the article is to reveal the problem (and to determine the possibility of solving the structural choice problem) as one of the areas in modern portfolio theory development. The article also argues that portfolio analysis is a method of structural analysis for various economic units. The research methodology is defined by the portfolio theory, optimization models implemented by the numerical gradient projection method, the empirical static method of analysis and simulation cases when the models are implemented. The research supported by the above- mentioned methodology aimed to reach the goal results in substantiating the structural choice. This choice differs from the classical portfolio choice as it is necessary to find how the investments are allocated for the portfolio units, and the same should be done for the characteristics points, where it is a challenge to apply the efficient set theorem, because different structures for the allocation of the resources, investments give the same or nearly the same combination of the expected return and total portfolio risk. Economic sectors characterized by the profitability and business risk are seen to be the portfolio units in terms of the macroeconomic approach from the portfolio theory developed by Tobin. Total income maximization model and total portfolio risk minimization demonstrate both the structural choice problem, including at the characteristic points, and choice dependence on the expansion of the resource allocated to the portfolio, and on the number of portfolio units. The analysis and model simulations enhance the efficient set theorem with the criteria for structural choice—income and risk correlation on the effective distribution curve, among other factors. A portfolio with two real sectors of the Russian economy illustrates that profitability and risk ratio determines the resource allocation between them under the income maximization model, so one sector grabs a more substantial resource. Thus, being a tool to support the structural choice, portfolio analysis gives structural diagnostics for the resource distribution, investments allocation by portfolio units.