- Nineteen-year-old Isis Obed Murillo died from a gunshot wound to the head on 5 July after members of the military fired live ammunition during a demonstration at Toncontín airport in Tegucigalpa. The military reportedly refused to co-operate with the investigation into his death.
- In August, 38-year-old teacher Roger Abraham Vallejo died in hospital as a result of injuries sustained from a bullet wound to the head, reportedly fired by police during the break-up of a protest in Tegucigalpa in July.
- In September, 16-year-old Gerson Ariel Cruz was seriously wounded by police following the break-up of a protest in Tegucigalpa. According to an eyewitness, the police chased protesters into a residential neighbourhood where they opened fire, shooting Gerson Ariel Cruz, who had taken no part in the protest. An investigation by the Special Prosecutor for Human Rights was under way at the end of the year.
Human rights defenders
Representatives of human rights organizations were threatened and harassed.
- In September, around 15 police officers fired tear gas canisters into the offices of the Committee of Relatives of the Disappeared in Honduras where scores of pro-Zelaya protesters had taken refuge. Around 100 people, including children, were inside the office at the time.
- In December, lesbian, gay, bisexual and transgender human rights activist Walter Tróchez was murdered in Tegucigalpa. Nine days earlier, he had escaped after being abducted by several masked men demanding the names and addresses of members of the opposition movement. His captors reportedly told him they had orders to kill him.
Freedom of expression and association
Several journalists were physically attacked. The de facto authorities closed Radio Globo and the television station Canal 36 intermittently from 28 June, though both media outlets were open again by the end of 2009. At times their offices were occupied by military personnel.
The de facto President issued a decree on 26 September permitting, amongst other things, the closure of newspapers and media outlets suspected of "insult[ing] public officials." Despite the fact that Congress had not passed the decree into law, police and military officials used it to authorize searches and closures of media outlets. The decree also stipulated that all public meetings or gatherings of any kind had to be authorized by the military or police in advance. The decree was revoked on 19 October.
- In September, on his way to cover events at Radio Globo and Canal 36, Delmer Membreño, a photographer for the newspaper El Libertador, was forced into a truck by four men in balaclavas. The men put a hood over his head and drove off. After 90 minutes, they stopped, dragged him out and put a gun to his head. One of the men told him that he was only being allowed to live so he could deliver a death threat to the director of El Libertador. The men then beat Delmer Membreño and burned his face and torso with cigarettes before releasing him. An investigation into the case was continuing at the end of the year.
Violence against women
Women demonstrators and women in custody reported sexual abuse and harassment by police officers. Many women reported being beaten on the buttocks and backs of the legs by police during demonstrations. No investigations were conducted into gender-based violence during the disturbances.