The most common and most disturbing criminal paternity cases are those involving the sexual abuse of a child. Laboratory testing is not possible in many of these cases because the abuser is a relative or close friend of the family, and the crime comes to light after the physical evidence is gone. Sometimes these unlawful sexual contacts do result in a pregnancy, especially if they continue over an extended period of time. In this instance, the DNA testing is usually routine and can be performed on the child or an abortus that is older than six weeks. DNA testing may be especially useful if there are closely related suspects, such as a father and son or two brothers. Criminal cases also may require the application of non-routine statistical and reporting techniques depending on the requirements of the court.

Cases where the victim of sexual abuse is underage rarely go to court. The offender usually will receive a lower prison term if he pleads guilty. Conviction in the face of DNA evidence is almost inevitable. In cases where the victim is an adult and consent is a defense, the defendant may change his story when he realizes that the DNA testing results are almost impossible to refute. The jury is usually unaware of this change of story and so often will vote to acquit the defendant.

DNA parentage testing has been questioned by the courts in only a handful of cases. Typically, less than 1 or 2 percent of civil cases result in a case contested in trial. The opportunity to have testing repeated by the same or another laboratory usually can settle most disputes to the satisfaction of all tested parties. In criminal cases, when the testing is scrutinized extensively in court, it is almost universally accepted.