Imprinting is the suppressing (or silencing) of certain genes on chromosomes, depending on which parent they were received from.

When DNA is passed to daughter cells after fertilization of an egg by a sperm, certain alleles can become active only if they were received from the mother, others only if they came from the father. If a gene is suppressed through imprinting from one parent, and the allele from the other parent is not expressed because of mutation, neither can act and the child will be deficient. A healthy child cannot be produced when both sets of chromosomes come from the same parent. Imprinting of the same areas will occur and all these genes will be suppressed.

A process known as reprogramming occurs in the parent female or male when the egg or sperm is maturing. In many instances this is achieved through methylation of the DNA of genes or regulatory sequences, which results in the gene not being expressed. In other instances, phosphorylation or other chemical modification of histone proteins appears to lead to silencing.

Imprinting is known to cause problems in cloning, with clones having DNA that is not methylated in the right places. Some scientists think this is due to there not being enough time for reprogramming to be properly achieved. When a nucleus is added to an egg during somatic cell nuclear transfer, the egg starts dividing in minutes, as compared to the days or months it takes for reprogramming during embryonic development. If time is the responsible factor, it may be possible to delay cell division in clones, giving time for proper reprogramming to occur.

Several genetic diseases that map to 15q13 (locus 3 of section 1 of the long arm of chromosome 15) in humans are due to abnormal imprinting. The Prader-Willi syndrome genes are expressed only when inherited from the father; the Angelman syndrome gene is expressed only when inherited from the mother. Thus, someone who inherits both chromosomes 15 from one parent (called uniparental disomy) has Prader-Willi or Angelman syndrome, depending on which parent they come from.

A gene in sheep called "callipyge" produces large buttocks consisting of muscle with very little fat. This gene is expressed only if it is on chromosome 18 inherited from the father and is not on the chromosome from the mother.