Myelodysplastic syndromes (MDS) and juvenile myelomonocytic leukemia (JMML) are rare clonal hematopoietic diseases presented in the childhood. Both diseases exhibit abnormal karyotype and/or monosomy of chromosome 7 in a subgroup of patients. We screened for copy number variations (CNVs) by array-comparative genomic hybridization (aCHG) the DNA from bone marrow of six MDS and four JMML pediatric patients. Array-CGH analysis identified five cases (50%) with monosomy 7, disclosing the chromosome 7 monosomy in two patients whose samples could not be evaluated by other methods. We identified CNVs in six patients, one of which displayed loss of LMO2, an oncogene that plays a central role in hematopoietic development. Our results suggest that array-CGH is a reliable and accurate technique to identify genomic alterations in MDS and JMML.