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Inclusion Criteria:

* Age: patients must be ≥ 1 and ≤ 21 years of age at the of study entry.
* Diagnosis:

  * Patients must have a diagnosis of first or second relapse or refractory acute myelogenous leukemia (AML) according to WHO classification with ≥ 5% blasts in the bone marrow, with or without extramedullary disease.
  * Patients may have CNS 1 or CNS 2 disease but not CNS 3.
* Performance Level: Karnofsky \> 50% for patients \> 16 years of age and Lansky \> 50% for patients ≤ 16 years of age.
* Prior Therapy:

  * Patients must have fully recovered from the acute toxic effects of all prior chemotherapy, immunotherapy, or radiotherapy prior to entering this study.
  * Patient has not received more than 2 previous induction attempts. (Frontline therapy is included in this count).
  * Patients must have adequate venous access.
  * At least 1 year must have elapsed since hematopoietic stem cell transplant (HSCT) and patients must not have active GVHD.
* Reproductive Function

  * Female patients of childbearing potential must have a negative serum pregnancy test confirmed within 2 weeks prior to enrollment.
  * Female patients with infants must agree not to breastfeed their infants while on this study.
  * Male and female patients of child-bearing potential must agree to use an effective method of contraception approved by the investigator during the study and for a minimum of 6 months after study treatment.
* Renal and Hepatic Function:

Patient must have adequate renal and hepatic functions as indicated by the following laboratory values:

* Patients must have a normal calculated creatinine clearance.

  * Pediatric Population (age \<18): Calculated creatinine clearance ≥ 90 ml/min/1.73m2 as calculated by the Schwartz formula for estimated glomerular filtration rate (GFR) where GFR (ml/min/1.73 m2) = k\*Height (cm)/serum creatinine (mg/dl). k is a proportionality constant which varies with age and is a function of urinary creatinine excretion per unit of body size; 0.45 up to 12 months of age; 0.55 children and adolescent girls; and 0.70 adolescent boys.
  * Adult Population (age ≥18): Serum creatinine ≤1.0 mg/dL; if serum creatinine \>1.0 mg/dL, then the estimated glomerular filtration rate (GFR) must be \>60 mL/min/1.73 m2 as calculated by the Modification of Diet in Renal Disease equation where Predicted GFR (ml/min/1.73 m2) = 186 x (Serum Creatinine)-1.154 x (age in years)-0.023 x (0.742 if patient is female) x (1.212 if patient is black.
* Total bilirubin \<1.5 x ULN for age and conjugated/direct serum bilirubin ≤ ULN for age if total bilirubin is elevated.
* Aspartate transaminase (AST)/alanine transaminase (ALT) ≤ 2.5 × ULN.
* Alkaline phosphatase ≤ 2.5 × ULN.

Exclusion Criteria:

* Patients with Down Syndrome.
* Prior treatment with Clofarabine.
* Previous history of veno-occlusive disease (VOD) or findings consistent with a diagnosis of VOD, defined as: conjugated serum bilirubin \> 1.4 mg/dL AND unexplained weight gain greater than 10% of baseline weight or ascites AND hepatomegaly or right upper quadrant pain without another explanation, OR reversal of portal vein flow on ultrasound, OR pathological confirmation of VOD on liver biopsy.
* Patients who have a history of cirrhosis of the liver or who are positive for hepatitis B core antibody (anti-HBc) or have a positive test for hepatitis C antibody (anti-HCV).
* Patient has received TBI.
* If it has been less than 1 year since the patient had a HSCT.
* Infection Criteria

  * Patients with a 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).
  * Positive blood culture within 48 hours of study registration.
  * Patient required supplemental oxygen or vasopressors within 48 hours of study (Oxygen after anesthesia for procedures is ok).
* Patient is receiving or plans to receive concomitant chemotherapy, radiation therapy, or immunotherapy other than as specified in the protocol.
* Use of investigational agents within 30 days or any anticancer therapy within 2 weeks before planned drug initiation with the exception of hydroxyurea or intrathecal therapy given with the diagnostic lumbar puncture.
* Have any other severe concurrent disease, or have a history of serious organ dysfunction or disease involving the heart, kidney, liver, or other organ system that may place the patient at undue risk to undergo treatment.
* Pregnant or lactating patients.
* Any significant concurrent disease, illness, psychiatric disorder or social issue that would compromise patient safety or compliance, interfere with consent, study participation, follow up, or interpretation of study results.
* Have had a diagnosis of another malignancy, unless the patient has been disease-free for at least 3 years following the completion of curative intent therapy with the following exceptions:

  * Patients with treated non-melanoma skin cancer, in situ carcinoma, or cervical intraepithelial neoplasia, regardless of the disease-free duration, are eligible for this study if definitive treatment for the condition has been completed.
  * Patients with organ-confined prostate cancer with no evidence of recurrent or progressive disease based on prostate-specific antigen (PSA) values are also eligible for this study if hormonal therapy has been initiated or a radical prostatectomy has been performed.

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