Despite decades of research, we do not know the functional significance of most sex differences in the brain. We are heavily invested in the idea that sex differences in brain structure cause sex differences in behavior. We rarely consider the possibility that sex differences in brain structure may also prevent sex differences in overt functions and behavior, by compensating for sex differences in physiological conditions, e.g. gonadal hormone levels that may generate undesirable sex differences if left unchecked. Such a dual function for sex differences is unlikely to be restricted to adult brains. This review will entertain the possibility that transient sex differences in gene expression in developing brains may cause permanent differences in brain structure but prevent them as well, by compensating for potentially differentiating effects of sex differences in gonadal hormone levels and sex chromosomal gene expression. Consistent application of this dual-function hypothesis will make the search for the functional significance of sex differences more productive.