Physiologically speaking, women and men are different – no real news flash there, but these differences even affect how we exercise and they haven't been studied for very long. 
Like most scientific studies, exercise studies were performed on men and the researchers assumed the results would cross gender line. About 15 years ago researchers began to study the female body in motion (FYI: Title IX passed over 35 years ago).
Here are a few of the differences they have found so far.
Exercise:
If you think of the calorie deficit created by exercise, it is similar to starvation. From an evolutionary perspective, exercise creates a physiological survival mode in women's bodies. The female metabolism slows down to maintain the ability to bear children in case of a famine.
The differences don't end there, so read more.
Weight Loss:
The evolutionary response to loss of calories explains why women have a more difficult time than men losing weight – just think of the Biggest Loser and the large amount of weekly pounds that men dropped. (Yay for this season's winner Ali, the first woman to ever win the contest). To lose weight women have to work harder.
Exercise for Weight Loss:
To efficiently and effectively use exercise as a weight loss tool women need to incorporate interval training since changes in pace and intensity force the body to work harder and burn more calories. Cross training is another way to kick exercise into high gear. The constant and continual mixture of disciplines confuses the body, making it hard to adapt to the variety of movement forms and ultimately burning more calories.
Lung Capacity
Women have smaller lungs than men and this size difference can inhibit women's tolerance for exercise and aerobic conditioning. Side by side, a man and a woman may be working out at the same level, but breathing may be more difficult for the women making the work feel even harder.
Estrogen
The female hormone estrogen is a major player in determining what fuels the body during exercise – fat versus carbs. Research also indicates that estrogen may fuel the competitive drive in women, seriously changing what it means to run like a girl.
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It's no fair!!!