The purpose of basic military training (BMT) is to enable the recruited soldiers to acquire basic military skills and develop the required physical fitness. This training is accompanied by heightened physical stress and the risk of injury and excessive stress symptoms (I&ESS). The objective of this study was to examine the extent to which the level of physical fitness at the beginning of BMT affects the incidence of I&ESS and resultant absence from duty. The data of a total of 774 subjects (age 20.5 ± 2.2) from 8 subsequent BMT quarters were analysed. The medical diagnoses made during the consulting hours of the unit physicians were reviewed for I&ESS and the kinds of injuries incurred and the sick leave pronounced were documented. The level of physical fitness per quarter was then categorised by means of the total numbers of points achieved during the standard basic fitness test (BFT). This categorisation was finally used as a basis for an analysis of the lost days in relation to the level of physical fitness. 255 of the 774 subjects (32.9%) suffered an I&ESS. 60% of all the I&ESS were located at lower extremity. There was a significant increase in the length of absence from duty among the group with the lowest level of physical fitness. The analysis revealed that the level of physical fitness at the beginning of BMT has a significant influence on the length of absence from duty due to I&ESS. Moreover, 60% of the injuries were lower extremity injuries, which show the specific significance they have for limitations during BMT. Overall, this reveals the necessity for appropriate preventive measures (additional fitness training, adjustment of requirements) to be implemented so that recruits with a low level of fitness can complete BMT with as few injuries as possible.