Most of the victims are men who have sex with other men (MSM) - whether they are gays or bisexuals - or transgender people.
But if Brazil and Mexico top the table of violence against men who have sex with men in Latin America, this may be because rights groups there monitor the situation more closely than elsewhere in Latin America. Much violence simply goes unreported elsewhere, gay activist organizations say.
"Brazil and Mexico are the only countries which have a register, which keep track of the murders. That does not mean necessarily that there is more violence there," says Arturo Díaz Betancourt of the Mexican National Council for the Prevention of Discrimination.
It is notable that when the United Nations Special Rapporteur on Extra-Judicial Killings made an official mission to Guatemala in 2006 his attention was drawn to a series of murders of gay and transgender people, and his subsequent report to the Human Rights Council stated "There has been impunity for murders motivated by hatred towards persons identifying as gay, lesbian, transgender, and transsexual. Credible information suggests that there were at least 35 such murders between 1996 and 2006. Given the lack of official statistics and the likely reticence if not ignorance of victims' family members, there is reason to believe that the actual numbers are significantly higher."
Many Latin American countries boast socially advanced legislation when it comes to defending sexual freedom and orientation. With law reform in Nicaragua and Panama over the past 12 months, there are now no states in Latin America which criminalize homosexual relations, for example.
Yet perhaps influenced by a lingering "machismo", prejudice and discrimination continue to flourish, whatever the laws say. Latin America is widely regarded as having a long way to go to successfully counter homophobia, or "fear or hatred of homosexuals."
"There is a real contrast between reality and theory. This is the developing region of the world with the highest number of laws against discrimination based on sexual orientation," says Dr. Ruben Mayorga, UNAIDS Country Coordinator for Argentina, Chile, Paraguay and Uruguay.
Aside from the individual pain homophobic attitudes inflict, the continuing stigma attached to same-sex relations is complicating hugely the task of slowing the spread of HIV in a region where sex between men is a leading mode of HIV transmission, health experts say.
Stigma and homophobia increase the isolation of gays, bisexuals and transgender people making them more reluctant to come forward, be identified and get advice.
"Homophobia represents a threat to public heath in Latin America," the Pan American Health Organization affirmed in a report. "This form of stigma and discrimination based on sexual orientation does not just affect the mental and physical health of the homosexual community, but contributes to the spread of the HIV epidemic."
UNAIDS has long campaigned against discrimination whether against those infected by the HIV virus or against a person for his or her sexual orientation.