Gene expression profiling has the potential to enhance current methods for the diagnosis of haematological malignancies. Here, we present data on 204 analyses from an international standardization programme that was conducted in 11 laboratories as a prephase to the Microarray Innovations in LEukemia (MILE) study. Each laboratory prepared two cell line samples, together with three replicate leukaemia patient lysates in two distinct stages: (i) a 5‐d course of protocol training, and (ii) independent proficiency testing. Unsupervised, supervised, and r² correlation analyses demonstrated that microarray analysis can be performed with remarkably high intra‐laboratory reproducibility and with comparable quality and reliability.