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Human rights defenders suffer extrajudicial executions, enforced disappearances, torture and ill-treatment as well as judicial harassment, threats and stigmatisation. Journalists, lawyers, prosecutors, those defending the rights of women, children, the lesbian, gay, bisexual, transgender and intersex (LGBTI) community, indigenous and Afro-Honduran communities, and those working on environmental and land rights issues are particularly at risk.

LGBTI defenders in Honduras are doubly discriminated against. They are discriminated firstly because they are human rights defenders and secondly because they defend LGBTI rights. Journalists continue to face increased risks as they report on human rights violations. Constant threats, harassment and killings of journalists have led many to self-censor. Since the 2009 military coup, the number of killings, threats and acts of intimidation against campesinos and environmental rights defenders has increased. The perpetrators of violations against many defenders of environmental, land and indigenous rights, are often influential landowners or logging companies.

On 4 June 2014 the Honduran Congress passed in first reading a draft for a proposed Law to Protect Journalists, Human Rights Defenders and Justice System workers (Ley de Protección para los Defensores de Derechos Humanos, Periodistas, Comunicadores Sociales y Operadores de Justicia). The draft provides for the establishment of a National Council on Protection, to be created within the government's Human Rights Secretariat and which should include representatives of relevant government departments and civil society, as well as of a new Directorate General in charge of providing protection measures. However, to date, there has been no improvement in security for HRDs.