Since the 2000s, Russian companies have actively begun to implement lean manufacturing tools. They allow you to identify weaknesses and reserves in the business processes of the company, identify their nature, identify the causes of competitive lag, giving employees effective options for corrective actions. Theoretically, their implementation is possible in any company, but in practice there are many features that impede the achievement of the planned result. For this reason, tools for improving business processes show different efficiencies depending on the conditions of their application. There are a large number of tools for finding reserves and eliminating losses in the production process – the construction of «lean production». They can be used individually and in combination with each other. This issue is especially relevant for multidisciplinary integrated structures, including cluster type. The authors of the article show the relevance of choosing tools to improve the organization’s business system, and search for points of growth in efficiency. A method for selecting a list of basic tools taking into account the typology of companies is determined. The company’s specificity assessment indicators are proposed that affect the selection of basic improvement tools. The considered methods of choosing tools for improving the business system have shown the relevance and necessity of using a list of basic tools. The proposed approach focuses on the choice of tools depending on the specifics of the business, the organization and composition of the products, which ensures the effectiveness of the changes, the rational use of time and labor. The purpose of the proposed approach is to formalize the procedure for optimizing the choice of tools for improving the organization’s business system in the structure of a multidisciplinary company. Improving the efficiency of business processes is the selection and implementation of one or more improvement tools, ensuring maximum enterprise performance, with restrictions on time and available resources for implementation and subsequent use (purchase of a software product, development costs, maintenance costs). The use of various tools to improve the business system allows you to select a balanced set of tools for a specific organization for solving actual business problems at the diagnostic stage. The universality of the approach used is presented in examples of various companies. As further research, it is proposed to describe the structure of the types of basic tools and the criteria for their application, to formulate a classification of all types of tools for improving the business system depending on the typology of the organization and the integrated structure.