However, during the 1990s, its reputation and integrity came under withering criticism, primarily due to the revelations of Special Agent Dr. Frederic Whitehurst, the most prominent whistleblower in the history of the Bureau.

Despite the budget limitations during the Great Depression, FBI director J. Edgar Hoover invested in major equipment upgrades including ultraviolet lamps, microscopes, moulage, and an extensive collection of tire treads, bullets, guns, and other materials that could assist local police in identifying crime scene evidence.

The Lab expanded to such an extent that the Forensic Science Research and Training Center (FSRTC) was established at the FBI Academy in Quantico, Virginia.

Whitehurst's whistleblowing in the 1990s and the adverse publicity trials, in which FBI Lab employees were revealed as incompetent or disingenuous, led to major changes.

The more widespread use of DNA testing in the late 20th century brought renewed scrutiny to the scientific reliability of many of the FBI Laboratory's forensic analyses.

[12] In a subsequent investigation in 2012, the DOJ found that evidence related to hair analysis had been falsified, altered, or suppressed, or that FBI agents had overstated the scientific basis of their testimony, to the detriment of defendants.

In 2015 the FBI reported that their expert witnesses overstated the reliability of hair analysis in matching suspects 96 percent of the time, likely influencing conviction of some defendants.

[13] In 2012, DNA testing revealed the innocence of three inmates from the District of Columbia who had been convicted to life and served years in prison based on hair analysis evidence and testimony by FBI experts.

He had been convicted of rape and murder and sentenced to life in part based on several FBI experts testifying to identification of him by bite-mark patterns, to a "medical certainty".

As the Washington Post reported, "No court in the United States has barred bite-mark evidence, despite 21 known wrongful convictions, a proposed moratorium in Texas and research showing that experts cannot consistently agree even on whether injuries are caused by human teeth.

"[14] This forensic test has been highly suspect for some years, but prosecutors and police continue to rely on it, and FBI agents make claims about it.