The objective of this study was to examine the effects on lower limb injury rates of adding structured balance and agility exercises to the 80-day basic training programme of army recruits. A blocked (stratified), cluster-randomised controlled trial was employed, with one intervention group (IG) and one control group (CG), in which 732 male and 47 female army recruits from the Australian Army Recruit Training Centre participated through to analysis. The IG performed specified balance and agility exercises in addition to normal physical training. The incidence of lower limb injury during basic training was used to measure effect. Analysis, which adhered to recommendations for this type of trial, used a weighted paired t-test based on the empirical logistic transform of the crude event rates. The intervention had no statistically significant effect on lower limb injury incidence (RR = 1.25, 95% CI 0.97-1.53, 90% CI 1.04-1.47), on knee and ankle injury incidence (RR = 1.08, 95% CI 0.83-1.38), and on knee and ankle ligament injury incidence (RR = 0.98, 95% CI 0.64-1.47). We conclude that the intervention, implemented in this fashion, is possibly harmful, with our best estimate of effect being a 25% increase in lower limb injury incidence rates. This type of structured balance and agility training added to normal military recruit physical training did not significantly reduce lower limb, knee and ankle, or knee and ankle ligament injury rates. Caution needs to be used when adding elements to training programmes with the aim of reducing injury, as fatigue associated with the addition may actually raise injury risk.