One advantage of sequestering all the boys into one PE class by themselves at the elementary school level is to allow boys and girls an equal opportunity to participate during competitive, team based, activities. According to a research paper by Julie A. Derry on the subject, girls sometimes feel that boys will monopolize game play among themselves on any given team. This leads to the girls' participation in the team's play to be marginalized. By separating boys from girls in such activities, girls can face fewer boundaries to fully participating in the activities.
Derry's paper also raises the point that in co-ed PE classes, boys will purposefully alter their level of play. Because of a perception (regardless of whether it is true or not) that girls are not as good as boys at sports, girls report that boys will purposefully lower their level of play to "accommodate" the girls. In single gender environments, there is no such perception that any such accommodation is necessary, leading to a fuller exercise experience for the students in each group.
Despite the fact that there are some advantages to having boys and girls in separate PE environments, it can reinforce the gender stereotype that girls are not as good at sports as boys. It is true that boys have a physiology that lends towards a greater baseline of strength, performance at competitive sports is just as much, if not more, about practice and skill. By segregating the two genders, it can send the false message to both the boys and the girls that girls cannot compete with boys.
One disadvantage to placing all the boys in one PE class and all the girls in another is the threat of legal challenges. National laws require that all students, regardless of gender or ethnicity, have equal access to educational opportunities; including physical educational opportunities. By segregating PE classes, schools open themselves to the possibility of a lawsuit claiming that girls are being denied the same quality of physical education that boys are receiving.