The Canada Research Chair program has a long-standing gender problem.
Way back in 2002, the CRC Secretariat commissioned a gender-based analysis of the program which concluded:
There are several sub-disciplines/fields where women are under represented among the Canada Research Chair nominees. In part, this may be due to the lesser "research maturity" of some disciplines where women are present in large proportion. In part, however, this under representation stems from the slow rate at which most universities have sought out and nominated women for Chairs, especially for Tier 2 Chairs.
The report concluded, however, that "overall, the Canada Research Chairs approval's [sic] process does not discriminate against women nominees".
In 2003, the Canadian Association of University Teachers formally complained to the Canadian Human Rights Commission about gender discrimination in the Canada Research Chairs program. The case was settled, but the overwhelming majority of CRC holders - especially Tier 1 and Canada Excellence Research Chairs -- are still men (see here for links and info about the human rights complaint).