Injuries during basic combat training (BCT) impact military health and readiness in the U.S. Army. Identifying risk factors is crucial for injury prevention, but few Army-wide studies to identify risk factors for injury during BCT have been completed to date. This study examines associations between individual and training-related characteristics and injuries during Army BCT. Using administrative data from the Total Army Injury and Health Outcomes Database (TAIHOD), we identified individuals who apparently entered BCT for the first time between 1 January 2002 and 30 September 2007, based on review of administrative records. Injuries were identified and categorized based on coded medical encounter data. When combined with dates of medical services, we could count injuries per person, identify unique injuries, and identify the quantity and type of medical care delivered. Regression models produced odds ratios (ORs) and 95% confidence intervals (CIs) to identify risk factors for injury during BCT (yes/no), adjusted for potential confounders. Of the 278,045 (83.4%) men and 55,302 (16.6%) women who were apparently first-time trainees, 39.5% (n = 109,760) of men and 60.9% (n = 33,699) of women were injured during training based on over 2 million recorded medical encounters entries. The large cohort yielded statistically significant, small magnitude associations between injury and all individual and training-related covariates for men, and all but medical accession waivers and weight for women. After adjustment, largest magnitude effects among men were due to age > 25 yr vs. 17-18 yr (OR = 1.83, 95% CI: 1.75, 1.91); having been married in the past vs. being single (OR = 1.36, 95% CI: 1.24, 1.49); rank E4-E7 vs. E1 (OR = 0.56, 95% CI: 0.53. 0.59); training at Ft. Jackson (OR = 0.66, 95% CI: 0.64, 0.69), Ft. Leonard Wood (OR = 0.67, 95% CI: 0.65, 0.70), or Ft. Knox (OR = 0.69, 95% CI: 066, 0.72) vs. Ft. Benning. Odds of injury were highest during 2005, 2006, and 2007. After adjustment for weight and body mass index, taller men had higher odds of BCT injury than average height men (OR = 1.08, 95% CI: 1.05, 1.11). Among women, short stature (OR = 1.11; 95% CI: 1.04, 1.19), training at Ft Leonard Wood (OR = 1.10; 95% CI: 1.04, 1.16) and evidence of injury prior to training based on accession waiver (OR = 1.12; 95% CI: 1.00, 1.26) increased injury risk. This Army-wide analysis reveals higher BCT-related injury rates for both men and women than prior studies and identifies risk factors for injuries during BCT. The large data set allows adjustment for many covariates, but because statistical analysis may yield significant findings for small differences, results must be interpreted based on minimally important differences determined by military and medical professionals. Results provide information that may be used to adapt training or medical screening and examination procedures for basic trainees.