Other than genetics and the difference in genitalia, arguably the largest biological difference between women and men is in the relative amounts of the primary reproductive hormones. In women, these are estrogen and progesterone and in men it is testosterone. Both sexes make all three hormones but the relatively amounts in adults differ significantly. On average women having roughly 1/10th to 1/30th the testosterone levels of men; men have similarly low levels of estrogen and progesterone. It would be patently absurd to pretend that this isn't impacting on the physiology of a woman versus a man directly in addition to any interaction with aspects of her genetic programming. .
A singular example is that women's bodies genetically form more of what are called pre-adipocytes (think of these as baby fat cells) in their lower bodies. These pre-adipocytes are stimulated to become fully formed fat cells and this occurs under the impact of hormones estrogen and progesterone with estrogen specifically impacting on the development of lower body fat cells in women. Even that doesn't occur until what might be described as one of the most profound times of life for both girls and boys occurs which is puberty. Prior to that, little girls and boys are more or less physically and physiologically identical. When there are differences they tend to be small and are generally in the same direction I mentioned above (i.e. girls are still slightly shorter or carry slightly more fat).
But it is at puberty, when the reproductive organs become active and hormonal levels diverge enormously that the primary physical and physiological differences between the sexes appear . A woman's specific physiology develops under the effects of estrogen and progesterone as does a male's under the influence of testosterone. Women develop their traditional body fat patterns, increasing not only total body fat but lower body fat specifically while men develop more muscle mass while losing fat. Effectively puberty is when the typical feminine and masculine physiologies develop and let me reiterate that I am using these terms only as descriptive shorthand with no implication about whether or not one is a relatively more or less appropriate or superior gender role than the other.
This is further shown by the fact that even small changes in hormones can have a profound impact. Even small changes in the levels of testosterone in women can drastically impact on her physiology, effectively masculinizing her in many ways.
Menopause is one of the most profound of those as through the process peri-menopause through the menopausal transition itself, her hormones drop from their youthful levels to nearly zero.
None of the above is meant to in any way dismiss the role of culture and environment in this. Clearly it plays a role and to ignore it is a mistake.
The above information is taken from the The Woman's Book by Lyle Mcdonald with Eric Elms