Glued-in rods are offering to timber joints not only enhanced stiffness and high load capacity but also aesthetical appearance and good fire resistance. However, no consistent manufacturing process and quality control method is reported in the literature. It is necessary to estimate the effect of possible manufacturing defects on pull-out behavior of glued-in rods. This paper presents the experimental results on glued-in rods with two types of possible manufacturing defects on site: eccentric position of rod in hole and inclined setting of rod in hole. The effect of manufacturing defects was investigated on the samples with three different glue-line thicknesses. A finite element model considering the elastic behavior of materials with their measured elastic parameters and dimensions is proposed. It illustrates the evolution of the stress distribution in the connection zone and explains the observed brittle failure modes.