The association between microchimerism acquired primarily through pregnancy and later disease is of increasing scientific interest. Because this line of research is new and little is known about the nature of microchimerism, studies of microchimerism are potentially vulnerable to error from confounding and reverse causation. To address the issue of confounding, we conducted an analysis of predictors of male microchimerism in 272 female participants of the Danish Diet, Cancer and Health cohort. Buffy coat DNA was tested for Y chromosome presence as a marker of male microchimerism. First, we used logistic regression and thereafter random forest modeling to evaluate the ability of a range of reproductive, lifestyle, hospital or clinic visit history, and other variables to predict whether women tested positive for male microchimerism. We found some indication that current use of contraceptive pills and hormone replacement therapy reduced the odds of testing positive for male microchimerism. However, prediction of male microchimerism presence was poor based on the available variables. Studies of the possible role of male microchimerism in maternal health and disease are therefore unlikely to be heavily confounded by the variables examined in the present investigation. More research focused on acquisition, retention and clearing of male cells in the maternal circulation is needed.