The article presents the results of the study focused on the elaboration of a method to identify knowledge deficits, particularly from the point of view of the implementation of make-to-order contracts in a machine-building enterprise. The study allowed to identify existing links between key elements of logistic customer service and knowledge processes implemented in selected polish machine-building industry enterprises. The proposed method enables to identify knowledge deficits and makes it possible to determine active actions to improve the level of logistic customer service. The research process consisted of two stages and was aimed primarily at acquiring qualitative information in the field of knowledge processes implemented in logistic processes concerning the execution of make-to-order contracts in a selected group of machine-building industry enterprises. The first stage was focused on the general determination of knowledge deficits in all logistic processes in analysed companies. The second stage was to characterize and structure identified deficits to get their sources and consequences basing on direct interviews with internal and external experts. The result of the research was the elaboration of a knowledge deficits matrix as an authorial method enabling the identification and evaluation of knowledge deficits in a machine-building enterprise. Hitherto, there have been the lack of elaborated methods for the identification of knowledge deficits in the processes of logistic costumer service, taking into consideration internal relations within a company, as well as external conditions and recipients’ requirements. The undertaken study allowed to identify main knowledge deficits in each logistic process, particularly in an order fulfilment process, in analysed machine-building industry enterprises. As a result, the study has resulted in elaborating the original tool, enabling the identification and evaluation of knowledge deficits in the form of a knowledge deficits matrix. The matrix allows to determine and structure knowledge deficits and to indicate key areas of actions improving the execution of customer orders in a machine-building enterprise. The specificity of machine-building enterprises requires an individual approach to knowledge management concerning logistic processes. The proposed method, even though it was elaborated for a determined group of companies, i.e. machine-building enterprises executing individual make-to-order contracts, includes versatile aspects and can be used in manufacturing companies, as well as in other companies, which are the participants of a supply chain. The application of an above-mentioned method allows to identify knowledge deficits in individual logistic processes, and as a result it makes possible to take active actions for improving logistic customer service.