Aerobic capacity in female athletes is typically 10% lower than male athletes when normalized for lean body mass. Factors contributing to a lower aerobic capacity in women are smaller hearts and thoracic cavities with smaller lung volumes, less blood volume, fewer red blood cells, and less hemoglobin. The gap in female endurance performance records compared to males is narrowing for marathons and triathlons, but may not equalize due to inherent differences in body composition and aerobic capacity.

Females have a lower maximal anaerobic threshold than males, which may be due to differences in muscle mass and/or training differences.

Pubertal and skeletal maturation is attained at a younger age in females. On average, men are taller and have wider shoulders with narrower pelvises than women. A wider pelvis in women contributes to an increased carrying angle at the elbows and Q-angle at the knees. Women have shorter limbs and a lower center of gravity, which may offer an advantage in improved balance.

Body fat percentage is greater in women than in men predominately due to a higher proportion of essential fat, which consists of sex-specific fat such as found in breasts, buttocks, and thighs. Storage fat is similar in both sexes.

In females, total muscle mass is about 25% of body weight compared with 40% in males, and females have smaller muscle fibers. Women have a similar proportion of fast- and slow-twitch muscle fibers and make similar gains in relative muscle strength with weight training. When controlled for body weight, women have less upper body strength and similar lower body strength compared to men. Testosterone effects cause greater muscle hypertrophy in men.

Bone stress injuries result from chronic repetitive training and can range from a stress reaction to a cortical fracture. Historically, these injuries are more common in certain populations of athletes with incidence of up to 21% in track-and-field athletes and 31% in military recruits, with a female preponderance. Several evidence-based grading scales utilizing MRI have been published, which can help to grade the bone stress reaction and predict return to activities. Higher grade bone stress injuries as assessed by MRI are associated with a prolonged recovery.

General training regiments advocate activity reduction to allow pain-free activities without advocating total rest. This can follow a progression of non-weight bearing on crutches (cross-training: swimming, stationary bike, flotation running), advancing to non-pounding, weight-bearing exercises (Stairmaster™, Vancouver, Washington, Nordic Track, Logan, Utah), with gradual re-entry into sport-specific activity. Sport-specific muscle rehabilitation, strengthening, and stretching are encouraged throughout. Low-grade stress fractures can heal with continuance of activities, using pain-to-guide activities.

More recently, it has been shown that risk factors associated with the Female Athlete Triad, in particular low bone mineral density and reduced numbers of menstrual cycles, are associated with a prolonged recovery in female athletes. Athletes with trabecular bone injuries (femoral neck, pubic bone, or sacrum) more often exhibit past or present disordered eating and oligomenorrhea/amenorrhea. Those with bone stress injuries at trabecular sites had a significantly lower bone mass at the lumbar spine, femoral neck, and total hip regions.