Meningococcal acquisition is a prerequisite for invasive disease. Three hundred and eleven male marine commando recruits were studied throughout 29 weeks of basic training to identify factors influencing meningococcal carriage and acquisition including troop number, season, smoking, respiratory infection, antibiotic usage and nasopharyngeal bacterial interference flora. A high carriage rate on entry to training (118/311, 37.9%) and subsequent sustained high rates of meningococcal acquisition were found. Of the potential factors examined, only active and passive smoking were found to be associated significantly with meningococcal carriage on entry. The association between active smoking and meningococcal carriage was dose-dependent, with odds ratios (OR) of 2.2 (95% CIs 1.0-4.8) and 7.2 (95% CIs 2.3-22.9) for light and heavy smokers respectively. Passive smoking predisposed independently to carriage (OR 1.8, 95% CIs 1.1-3.0). Active and passive smoking combined to give an attributable risk for meningococcal carriage of 33%. In contrast, despite a high and sustained rate of meningococcal acquisition in the study population, none of the risk factors investigated, including active smoking, was associated significantly with meningococcal acquisition. No cases of meningococcal disease occurred during the 16-month study period. Therefore smoking may increase the duration of meningococcal carriage rather than the rate of acquisition, consistent with the increased risk of meningococcal disease from passive as opposed to active smoking. Public health measures that reduce the prevalence of smoking should reduce the risk of meningococcal disease.