In the flange connection, geometric imperfections of flatness appear during the manufacturing process. They affect the increase of forces in the bolt connection and tubular structure, which negatively affect the occurrence of fatigue fractures. To perform the analysis, an FEM model was built taking into account existing standards and guidelines (e.g. German DIBt, ISO 7090, VDI 2230, etc.). Various forms of geometric imperfections were simulated with purpose-built code. It was found that the force in the bolt in the area of geometric imperfection increases regardless of its shape and size. The external force on the flange connection is no longer redistributed evenly between the bolts as in the case of an ideal flange. At the same time, the sum of all forces in the bolts with the geometric imperfection on the flange included is equal to the external force. Procedure under consideration makes it possible to set upper limits in determining the permissible geometric imperfections.