We report that gene fusions are present in 65% of BCP ALL, and identify several new fusions and two novel subtypes; one characterized by recurrent IGH-DUX4 or ERG-DUX4 fusions and one characterized by an ETV6-RUNX1-like gene-expression profile, and coexisting ETV6 and IKZF1 alterations. Here, ETV6 is linked to acute lymphoblastic leukemia.