Clofarabine, Idarubicin, and Cytarabine (CIA) Versus Fludarabine, Idarubicin, and Cytarabine (FLAI) in Acute Myelogenous Leukemia (AML) and High-Risk Myelodysplastic Syndrome

Inclusion Criteria:

1. Sign an Institutional Review Board (IRB)-approved informed consent document.
2. Age 18 to 60. Patients above the age of 60 only with principal investigator (PI) approval
3. Diagnosis of newly diagnosed AML \[other than acute promyelocytic leukemia (APL)\] or high-risk (intermediate-2 or high by International Prostate Symptom Score (IPSS) or \> 10% blasts, including CMML) MDS. Prior therapy with hydrea and the use of a single or a two day dose of cytarabine (up to 3 g/m2) for emergency use up to 24 hours prior to start of study therapy is allowed. Prior therapy for MDS or other AHD is not allowed.
4. Eastern Cooperative Oncology Group (ECOG) performance status of \</= 3 at study entry.
5. Organ function as defined below (unless due to leukemia): Serum creatinine \</= 3 mg/dL Total bilirubin \</= 2.5 mg/dL , Alanine aminotransferase (ALT) (SGPT) \</= 3 \* upper limit of normal (ULN) or \</= 5 \* ULN if related to disease.
6. Women of childbearing potential must have a negative serum or urine pregnancy test within 7 days and must agree to practice acceptable contraceptive methods. Men must agree not to father a child and agree to use a condom if his partner is of child bearing potential.
7. Cardiac ejection fraction \>/= 40% (by either cardiac echo or multiple gated acquisition scan (MUGA) scan). Documentation of recent (\</= 6 months from screening) outside reports is acceptable.

Exclusion Criteria:

1. Breast feeding females
2. Patients with uncontrolled active infections (viral, bacterial, and fungal are not eligible).
3. Patients with active secondary malignancy will not be eligible.