Clofarabine, Cyclophosphamide and Etoposide for Minimal Residual Disease Positive Acute Leukemia

Inclusion Criteria: * Diagnosis of acute lymphoblastic leukemia (ALL) or acute myeloid leukemia (AML) with \<5% blasts in the bone marrow (M1) by morphology and that meets one of the following criteria: * Flow cytometric evidence of MRD (≥ 0.1% leukemic blasts for ALL or \<5% leukemic blasts for AML detected in the bone marrow) OR * Molecular/cytogenetic evidence of disease (FISH or PCR methodology) performed within 7 days * AND with the intent of going on to an allogeneic hematopoietic cell transplantation (allo-HCT) independent of this study * Age 0 to 60 years * Karnofsky Performance Status ≥ 50% for patients 16 years and older and Lansky Play Score ≥ 50 for patients under 16 years of age * Patients must have a life expectancy ≥ 8 weeks as determined by the enrolling investigator * Have acceptable organ function as defined within 7 days of study registration: * Renal: creatinine clearance ≥70mL/min/1.73m2 or serum creatinine based on age/gender * Hepatic: aspartate aminotransferase (ALT) \< 5 x upper limit of normal (ULN) and total bilirubin ≤ 1.5 x upper limit of normal (ULN) for age * Cardiac: left ventricular ejection fraction ≥ 40% by echocardiogram (ECHO/MUGA) * Patients must have fully recovered from the acute toxic effects of all prior chemotherapy, immunotherapy, or radiotherapy prior to entering this study. At least 14 days must have elapsed from prior chemotherapy; at least 7 days must have elapsed since receiving biological therapy. Hematopoietic growth factors: At least 7 days since the completion of therapy with a growth factor and at least 14 days since pegfilgrastim (Neulasta®) administration. * Sexually active females of child bearing potential must agree to use adequate contraception (diaphragm, birth control pills, injections, intrauterine device \[IUD\], surgical sterilization, subcutaneous implants, or abstinence, etc.) for the duration of treatment and for 2 months after the last dose of chemotherapy. Sexually active men must agree to use barrier contraceptive for the duration of treatment and for 2 months after the last dose of chemotherapy. * Voluntary written consent before performance of any study-related procedure not part of normal medical care, with the understanding that consent may be withdrawn by the subject at any time without prejudice to future medical care Exclusion Criteria: * Acute Promyelocytic Leukemia (APL) * Active central nervous system (CNS) leukemia or known chloromatous disease * Receiving or plans to receive concomitant chemotherapy, radiation therapy; immunotherapy or other anti-cancer therapy other than is specified in the protocol * Systemic fungal, bacterial, viral, or other infection not controlled (defined as exhibiting ongoing signs/symptoms related to the infection and without improvement, despite appropriate antibiotics or other treatment) * Pregnant or lactating. The agents used in this study are known to be teratogenic to a fetus and there is no information on the excretion of agents into breast milk. All females of childbearing potential must have a blood test or urine study within 2 weeks prior to registration to rule out pregnancy. * Known allergy to any of the agents or their ingredients used in this study