Cigarette smoking has been reported to be prevalent in military training populations, and associated with lower cardiorespiratory fitness and higher risk of training-related injury. However, it is unclear whether habitual smoking impairs development of physical fitness. It is possible that smoking-induced alterations in oxidative stress, inflammation and hormone balance may disrupt training adaptation in smokers. The aim of this programme of work was to identify the influences of smoking on physical performance adaptation, selected biomarkers and injury risk in a military trainee population. The first study established that habitual smokers comprised 48% of a cohort of 2087 trainees. Upon closer examination, both at entry (Study 2) and during 10 weeks of training (Study 3) smokers exhibited chronically elevated oxidative stress and, after commencement of training, evidence of significantly higher resting inflammation compared with non-smokers. Throughout the full duration of training, performance of smokers in military physical fitness tests was significantly worse than non-smokers (Study 4), but neither muscular adaptation nor physical performance improvement were impaired in smokers in the early stages (10-14 weeks) or over the full duration (26 weeks) of training. It was expected that smokers would experience greater acute inflammatory responses to exercise but neither these, nor hormonal responses, differed between smokers and non-smokers in response to consecutive days of military field exercise (Study 5). In addition to poorer physical performance in smokers, training-related injury incidence was higher in smokers than non-smokers, specifically injuries attributed to overuse (Study 6). Overall, smoking appears to cause some physiological alterations which, while not impairing adaptation to training, may have adverse implications on health outcomes. Although the specific underlying mechanisms are unclear, habitual smokers exhibit greater injury risk and typically lower physical fitness than non-smoking counterparts.