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This paper proposes an adaptive randomisation procedure for two-stage randomised controlled trials. The method uses data from a first-wave experiment in order to determine how to stratify in a second wave of the experiment, where the objective is to minimise the variance of an estimator for the average treatment effect. We consider selection from a class of stratified randomisation procedures which we call stratification trees: these are procedures whose strata can be represented as decision trees, with differing treatment assignment probabilities across strata. By using the first wave to estimate a stratification tree, we simultaneously select which covariates to use for stratification, how to stratify over these covariates, and the assignment probabilities within these strata. Our main result shows that using this randomisation procedure with an appropriate estimator results in an asymptotic variance which is minimal in the class of stratification trees. Moreover, our results are able to accommodate a large class of assignment mechanisms within strata, including stratified block randomisation. In a simulation study, we find that our method, paired with an appropriate cross-validation procedure, can improve on ad-hoc choices of stratification. We conclude by applying our method to the study in Karlan and Wood (2017, Journal of Behavioral and Experimental Economics , vol. 66, 1–8), where we estimate stratification trees using the first wave of their experiment. [ABSTRACT FROM AUTHOR]