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In pediatric medicine, there are two references that involve this word.
Harlequin color change
Harlequin color change is an unusual but rather dramatic skin coloration change of the newborn during the first few minutes of life. It might be observed in the delivery room or shortly thereafter. When the infant is placed on his or her side, there is a dramatic and sharp demarcation in color between one side of the body and the other. One side (the lower if the baby is on its side) is bright red; the other side is pale. The line of demarcation is strikingly sharp and exactly bisects the body down the middle. This color change only lasts a few minutes, and may only involve the face or trunk. It is caused by immaturity of the nervous system's control over blood vessel dilatation in the skin. It is totally harmless, and merely a medical curiosity with no permanent effects whatsoever.
Harlequin fetus refers to a rare autosomal recessive genetic disorder of skin formation. It is a severely disfiguring disorder involving thickened, ridged, and cracked skin forming horny plates over the entire body, distorting the facial features and constricting the digits. It is usually fatal in the first few days of life. It can be prenatally diagnosed in mothers who have a family history of the disease.