In this work, we characterized the miRNome of LSC-enriched CD34+CD38−CD26+ fraction (BCR-ABL1+) and its BCR-ABL1− counterpart (CD34+CD38−CD26− fraction, defined as “CML-CP HSC” in this article) isolated by fluorescence-activated cell sorting (FACS) from CML-CP patients at diagnosis by small RNA-Next-Generation Sequencing (NGS), in order to identify differential molecular mechanisms that contribute to unravel LSC biology, and the possible therapeutic implications of such differences. Here, CD34 is linked to chronic myelogenous leukemia, BCR-ABL1 positive.