Stress fractures represent one of the most common and serious overuse injuries in the military environment. The aim of this prospective study was to determine the incidence of stress fractures during 12 weeks of Basic Training (BT) by comparing the results of the intrinsic risk indicators obtained from a group of participants who suffered stress fractures, with the rest of the original group (controls) who did not suffer from any stress fractures, and to assess any changes in physical markers whilst following a progressive, scientifically designed, Physical Training (PT) Programme during the BT. The intrinsic risk factors investigated included sex, age, race (measured via questionnaire), foot morphology (wet test), Q angle, leg length discrepancy, bone density (dual-energy X-ray absorptiometry(DEXA), physical fitness (standardized military fitness test, isokinetic upper and lower leg strength, handgrip strength), flexibility (ankle plantarflexion and dorsiflexion, hip internal and external rotation), anthropometry (skinfold method and DEXA), female menstrual disturbances and lifestyle behaviours including smoking, female contraception use and medical history of previous injury (questionnaire). The cohort (n=183), also refered to as the Experimental Group (EG), was measured at the beginning and at the end of the BT period. The standardized physical fitness test was also completed in the fifth week of training. The latter’s results were compared to the results obtained by a Control Group (CG), who had undergone BT the year prior to this cohort. The size of the cohort, the intrinsic risk factor profile and the control of certain extrinsic risk factors may have contributed to zero incidences of stress fractures found. Within the intrinsic risk factor profile, sex, age, race, foot morphology, Q angle, hip external rotation and bone density were normal whilst the measured leg discrepancy and limited ankle dorsiflexion appeared to not have a sufficient risk for stress fracture development. The small sample of the cohort that reported having menstrual irregularities, smoked and had a history of previous fractures, did not place this cohort at risk for stress fracture development. The cohort did, however have lower isotonic, isokinetic and isometric strengths than the other cohorts who reported a relatively high stress fracture incidence. The BT period found statistically significant changes in bone density, flexibility, body composition, muscle strength and endurance. Female participants showed an increase in the T- and Z-scores of the left femur area, a deterioration in left ankle dorsiflexion and hip external rotation, whilst their plantarflexion increased. Their mesomorph component increased, and decreases in % body fat (BF) as well as in the ectomorph and endomorph component were also found. Male participants’ plantarflexion and hip external rotation decreased whilst their dorsiflexion increased. Lean body mass and mesomorph component increased whilst %BF, ectomorph and endomorph component decreased. The new cyclic-progressive PT programme controlled for risk of injury by allowing sufficient periods of recovery, by gradually increasing the duration, frequency, and intensity of training, by reducing repetitive weight-bearing activities and by including a variation of exercises. Running shoes, rather than combat boots, were also worn during PT. Marching on concrete was eliminated. Significant improvements were shown by both male and female participants in aerobic fitness and muscular endurance and muscular strength. Future research should include a larger size cohort, who developed stress fractures utilising BT groups from different corps and units in the South African Military environment. Other potential extrinsic risk factors, such as surface and equipment, should also be investigated.