The 17q21.31 microdeletion syndrome is characterized by intellectual disability, epilepsy, facial dysmorphism and friendly behavior. Recently, KANSLJ gene has been considered as a major causal gene for this phenotype. Here we report on two Turkish patients with different seizure types and additional dysmorphic features associated with 17q21.31 microdeletion syndrome. A 4 year-old female patient with generalized tonic-clonic seizures, mild mental retardation, dysmorphic features and friendly behavior and a 14 years-old female with intractable epilepsy, different dysmorphic features, severe mental and motor retardation and self-mutilation were evaluated by array-based comparative genomic hybridization (microarray CGH). Array CGH identified 17q21.31 microdeletion that contains MAP7 CRHR1, KANSLI, PLEKHMI genes in case I and CRHR1, PLEKHM but not KANSLJgenes in case 2. To the best of our knowledge this is the first report of a patient with the 17q21.31 microdeletion which does not encompass KANSLI gene. These data imply another gene or genes causing similar phenotype in this patient.