The American Civil Liberties Union, the ACLU of the Nation's Capital, the ACLU of Kansas and civilian defense counsel David E. Coombs have filed a lawsuit on behalf of Chelsea Manning in federal court in the District of Columbia against Secretary of Defense Chuck Hagel and other Department of Defense (DOD) and Department of the Army officials for their failure to provide necessary medical treatment for her gender dysphoria, a condition with which she was originally diagnosed by Army doctors more than four years ago.

On June 14, 2016, the American Civil Liberties Union, along with the ACLU of Northern California, and the firms Orrick, Herrington & Sutcliffe and Van Der Hout, Brigagliano & Nightingale, have filed a settlement agreement in the class-action suit Lyon v. the U.S. Immigration Customs and Enforcement agency (ICE). The settlement requires the agency to give detainees at four Northern California immigrant detention facilities improved access to telephones, including creating private spaces for free and direct calls, delivering phone messages, removing arbitrarily short limits on call duration, and making accommodations for indigent immigrants.

In June 2015, a federal court decided in favor of the ACLU position in Walnut Grove. With this federal court ruling, the Mississippi Department of Corrections will be held accountable to their Constitutional mandate to protect the prisoners of Walnut Grove from violence. A victory for prisoner's rights, this decision marks a major blow to the for-profit industrial complex. In April 2015, in federal court, the ACLU National Prison Project, the Southern Poverty Law Center, and McDuff & Byrd are all participating in a hearing that seeks to prove that the Mississippi Department of Corrections is violating the Eighth Amendment rights of all prisoners at Walnut Grove Correctional Facility to protection from violence. The department contracts with a for-profit prison operator, Management and Training Corporation (MTC), to run Walnut Grove. Over the years it has been proven that MTC has failed to implement fundamental security measures to ensure prisoner safety, which resulted in two major riots in 2014 that left 25 prisoners seriously injured. Three years ago, the Mississippi Department of Corrections agreed to take specific measures to reduce the violence at Walnut Grove when it settled a federal lawsuit brought by the ACLU National Prison Project and the Southern Poverty Law Center. The 2012 case decided that children under the supervision of the Mississippi Department of Corrections (MDOC) would no longer be housed in a privately run prison or subjected to brutal solitary confinement. The lawsuit charged that conditions at the Walnut Grove Youth Correctional Facility, operated by GEO Group, Inc., were unconstitutional.

Whether the Constitution protects pretrial detainees against the unreasonable use of force regardless of the subjective motivation of the guards using that force.

A federal judge has ruled that the Alabama Department of Corrections (ADOC) can no longer discriminate against prisoners living with HIV by housing them separately from all other prisoners and categorically denying them equal access to prison rehabilitative programs, according to a landmark decision in a lawsuit filed by the ACLU National Prison Project, the AIDS Project, and the ACLU of Alabama. This ruling paves the way for prisoners living with HIV to have access to needed and appropriate services, and to the classes and training available to other prisoners.