To avoid missing potential drug usage, urine drug screen testing typically occurs tri-weekly on random days of the work week. Drug laboratories specializing in physician health programs must perform a much wider spectrum of drugs than the typical workplace environment. In addition to the traditional drugs of abuse (cocaine, heroin, amphetamines, marijuana, ethyl alcohol, etc.), physician health programs must also test for prescription opioids, (oxycodone, hydromorphone, etc), anesthetics (e.g., fentanyl), novel antidepressants (e.g., trazodone), and indicators of long-term alcohol exposure (e.g., ethylglucuronide). Because poppy seeds can produce a positive result for opiates, individuals enrolled in these programs are instructed to avoid food products containing these seeds, although a marker for poppy seed use (thebaine) has been validated. Testing must also be conducted for the presence of adulterants and substitution of urine, although the institution of same-gender witnessed urine collection minimizes but not eliminates this practice.

Samples containing positive results on urine screen must be confirmed by some form of mass spectrometry (GC/MS, GC/MS/MS, LC/MS or LC/MS/MS), as results may be challenged by the physician. Chain-of-custody documentation is also a requisite for testing laboratories. Some programs are experimenting with alternate samples such as blood, oral fluids, hair, and sweat. While these matrices offer some advantages to the program including longer duration of positivity and more convenient sampling, they are more difficult for the toxicology laboratories to establish.