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This paper discusses the optimization of warehouse management in the assembly and distribution company. As part of complex logistics system, warehouse management plays a significant role in every company, connecting the areas of storage, material flow, production, record keeping and dispatch with the company´s economic objectives. It also has a significant impact on business operations and can be of an important competitive advantage. It may be argued that well-managed logistics, including a continuous material flow, cost minimization as well as overall streamlining of individual processes associated with manufacturing of products, are powerful strategic tools for companies and lead to their strong market position. It is almost an imperative for them to use modern knowledge in this area and strive for improvement. After the introducing chapters, paper includes an optimization proposal using particular methods of multi-criteria evaluation of variants which consists of determining the criteria for variants evaluation, developing the basic multi-criteria matrix and selecting as well as applying the specific method for final evaluation (in our case, the comparison with WSA and TOPSIS methods has been carried out). Final part of the paper outlines the most appropriate option regarding the introduction of an automatic identification system to optimize the warehouse management system.