Constitutional chromosomal aberrations are inborn changes with or without phenotypic consequences. Conventional chromosome analysis has been for a long time the method of choice for identification of such abnormalities. However, over the past decades, several molecular cytogenetic techniques have successfully been introduced into the genetic diagnostic laboratories to increase the detection sensitivity and to outline chromosome rearrangements in more detail. Each method has its strength and limitation, therefore often several techniques are needed to detect and unravel the complexity of chromosome abnormalities. This chapter focuses on the most commonly used methods in the diagnostic setting for detection and characterization of constitutional chromosome abnormalities.