In 2003, Hellerstein agreed to hear a consolidated master case against three airlines, ICTS International NV, and Pinkerton's airport security firms, the World Trade Center owners, and Boeing Co., the aircraft manufacturer. The case was brought by people injured in the 9-11 attacks, representatives of those who died, and entities that suffered property damage. In September 2004, just before the three-year statute of limitations expired, the insurers for the World Trade Center filed suit against American Airlines, United Airlines, and Pinkerton's airport security firm, alleging their negligence allowed the planes to be hijacked. On January 12, 2006, Hellerstein dismissed the last remaining property-damage claim against New York City, while leaving pending several other suits against other parties, among them the Port Authority of New York and New Jersey. According to Reuters, "ix insurers sought repayment from the city for expenses arising from the collapse of a 47-story office building near the Twin Towers"; Hellerstein ruled New York had sovereign immunity. The World Trade Center first responders and the city conflicted with each other over the issue of payments for health costs of survivors among the first responders. On October 17, 2006, Hellerstein rejected New York City's motion to dismiss lawsuits that requested health payments to the first responders. Hellerstein, on July 7, 2008, ruled that
"the city is not required to re-sift through debris from ground zero in search of bits of human remains and remove it to a space where a cemetery might be built. Plaintiffs have no property right in an undifferentiated, unidentifiable mass of dirt that may or may not contain the remains of plaintiffs' loved ones. Not every wrong can be addressed through the judicial process."
Hellerstein urged the city to build a memorial and nature reserve at the site. Victims' families' counsel Norman Siegel criticized the ruling: "We are not prepared to leave hundreds of human remains of 9/11 victims on top of a garbage dump as their final resting place."
U.S. military detainees
On December 20, 2004, Hellerstein said he would deny a government request to delay a review of whether certain Central Intelligence Agency internal files related to Iraq should be made public. On June 3, 2005, Hellerstein ordered the government to release four videos from Abu Ghraib prison and dozens of photographs from the same collection as photos that touched off the Iraqi prisoner abuse scandal a year prior. Hellerstein said the 144 pictures and videos could be turned over in redacted form to protect the victims' identities. The judge ordered the release after he viewed eight of the photos. They were given to the Army by a military policeman assigned to Abu Ghraib. On September 29, 2005, in ACLU v. Department of Defense, Hellerstein ordered the release of 87 more photographs and videotapes. In January and September 2017, Hellerstein ordered the release of additional government documents, including those referred to in the Senate torture report.
Hope poster case
Hellerstein presided over the Barack Obama "Hope" poster case. Shepard Fairey, the artist behind the poster, sued the Associated Press. He sought to establish that his Hope poster did not infringe the AP's copyright of a shot taken by AP freelancer Mannie Garcia. The AP countersued, accusing Fairey of infringement. When Fairey finally admitted to his attempted cover up, Hellerstein allowed Fairey's original counsel to withdraw. In January 2011, the AP and Shepard Fairey settled out of court.
Hellerstein presided over the Harvey Weinstein case. In April 2019, Hellerstein eliminated 17 claims from the case, but allowed the case to proceed to trial.
On July 23, 2020, Hellerstein granted a temporary restraining order in favor of President Donald Trump's former attorney Michael Cohen, ordering that Cohen be released from prison into home confinement. Cohen had argued that prison officials were preventing his transfer to home confinement out of retaliation for Cohen's refusal to agree not to write a book or contact the media while in home confinement.