The German medical journal Deutsches Ärzteblatt did an analysis of the percentage of female first authors over the last 50 years (https://web.archive.org/web/20120611085236/http://www.aerzteblatt.de/int/article.asp?id=60949?). The number was 0-4% as recently as 25 years ago, but there has been a yearly increase to 18% last year (see this figure (https://web.archive.org/web/20120611085236/http://www.aerzteblatt.de/int/bild.asp?id=24380?)), both for submitted and accepted manuscripts. This number corresponds to the percentage of female senior faculty in Germany, but 64% of students starting to study medicine last year were women. A similar increase – although to higher numbers – has been seen in biology (see this study (https://web.archive.org/web/20120611085236/http://dx.doi.org/10.1002/ajhb.10160?)).
These numbers seem to indicate that women are neither less likely nor more likely to have a manuscript accepted. Unless you assume that women are more often denied first authorship than men. But I was surprised to learn how little progress had been made between 1957 and 1982. This study (https://web.archive.org/web/20120611085236/http://content.nejm.org/cgi/content/full/355/3/281?) of female first and senior authorship in American medical journals probably gives the explanation. The numbers of female medical students didn't start to rise until the 1970s, and they probably started to write their first papers about ten years later. Which would mean that in another 25 years female first and senior authors in medical journals should be as common as their male colleagues. Isn't that a bit long in the future?