Is there a way of performing stratified cross validation using xgboost module in python?
What you are doing is a typical example of k-fold cross validation.

XGBoost is just used for boosting the performance and signifies "distributed gradient boosting".

First, run the cross-validation step:

kfld = sklearn.cross_validation.KFold(labels.size, n_folds=10)


Then, use the train and test indices in kfld for constructing the XGBoost matrix and re-scaling weights by looping over them(the indices).

A very neat implementation has been given as a Kaggle example here.

So, cross validation is not done with the xgboost package, it is done with the cross_validation module of sklearn, and then the gradient boosting is done on the indices of the k-fold validation variable results.