Mr Gilmore said Benedict XVI should "temper" his language as his hard-line stance encouraged discrimination.
"We have many examples of where there is not only discrimination against gay people, but there has been nasty homophobic bullying and assaults on gay people and I think opinions like that give comfort to that," he told the Irish Examiner.
Mr Gilmore urged the Pope and others in positions of influence to "bear in mind" the effects of their language when dealing with the issue after the Pope sparked controversy with a spate of anti-gay statements, including one in which he said "saving" humanity from homosexual behaviour is just as important as saving the rainforests.
Research by the Gay and Lesbian Equality Network (GLEN) shows that 80.4% of Irish gay, lesbian and transgender people reported facing homophobic verbal abuse, 42.5% said they had been threatened with physical violence, 24.4% reported being punched, kicked or beaten, and 7.9% said they had been attacked with a weapon.
The Catholic Church teaches that while homosexuality is not sinful, homosexual acts are. Its opposition to any move towards gay marriage saw Irish Catholic bishops call for a free vote on civil partnership legislation in the Dáil this week as the proposals would see same-sex couples get some of the rights afforded to heterosexual couples if passed.
Mr Gilmore made it clear that "legislators should legislate" and Church and state should be kept separate.
In a wide-ranging interview with the Irish Examiner as an opinion poll showed he was the first choice for Taoiseach with 40% of the electorate, Mr Gilmore insisted he could only become head of Government in a coalition if Labour gained more seats than Fine Gael at the next general election as he was "not into" a compromise such as rotating the office with Enda Kenny in a post-election deal.
Mr Gilmore also warned Fianna Fáil not to try and regain support by fighting dirty at the next election and dismissed repeated attacks from opponents that his success in the polls was due to him avoiding taking unpopular positions on national issues.
The Labour leader also came out strongly against any form of water charging for the first time, and he voiced public opposition to the extradition of former official IRA boss Seán Garland to the United States on counterfeiting allegations.
Green leader John Gormley has also called for the Catholic Church not to become involved in parliamentary matters regarding civil partnerships.
The Irish Catholic Bishops’ Conference was unavailable for comment.
Source: Irish Examiner