The similarities between all humans is in their 23 pairs of matched chromosomes made up of many thousands of genes.    We are bi-lateral, bipedal, have a head with a large, complex brain, a spine, a torso, two arms, two legs.  The main  difference is in the hormones--testosterone or estrogen/progesterone (the sex organs are built from the same system as can be seen in the development in the womb).  
The difference between men and women is in the 23rd chromosome--the XX chromosome has two complete pairs of genes; the  XY chromosome has about two-thirds matched genes and one-third is missing the matching genes in that chromosome--much like a Y is an X without one of the 4 arms..  

Yes, of course men and women are "different"-- but the similarities far outweigh the differences.