Diagnosis of mitochondrial disorders has been difficult due to the clinical and genetic heterogeneity, as well as unique features of mitochondrial genetics. Definitive diagnosis requires the identification of molecular defects in either the mitochondrial or the nuclear genome. We describe the clinical and molecular characteristic of some common mitochondrial syndromes and molecular methodologies available for the detection of mitochondrial DNA mutations. This review provides overview of current molecular diagnosis of mitochondrial DNA disorders that is useful in patient care and genetic counseling. Diagnosis of mitochondrial disorders has been difficult due to the clinical and genetic heterogeneity, as well as unique features of mitochondrial genetics. Definitive diagnosis requires the identification of molecular defects in either the mitochondrial or the nuclear genome. We describe the clinical and molecular characteristic of some common mitochondrial syndromes and molecular methodologies available for the detection of mitochondrial DNA mutations. This review provides overview of current molecular diagnosis of mitochondrial DNA disorders that is useful in patient care and genetic counseling.