The other gene is linked to thyroid function, which is an area previously been linked with sexual orientation, according to the authors of the study.
While some genetic differences were found in these areas, the researchers have cautioned that the results are "best described as speculative", but still leave researchers a step closer to understanding how sexual preferences develop.
"Because sexuality is an essential part of human life — for individuals and society — it is important to understand the development and expression of human sexual orientation," lead author Dr Alan Sanders told The Telegraph.
"The goal of this study was to search for genetic underpinnings of male sexual orientation, and thus ultimately increase our knowledge of biological mechanisms underlying sexual orientation."
He added: "What we have accomplished is a first step for genome wide study on the trait, and we hope that subsequent larger studies will further illuminate its genetic contributions."
The purpose of genome-wide studies such as this one is to find variations in DNA that are linked to a specific trait, in this case homosexuality.
But other studies usually use a much larger subject group, often including more than 100,000 people, with a smaller group possibly indicating a less reliable overview of the population as a whole.
Dr Nina McCarthy of the University of Western Australia told Cosmos that "findings from small studies are less likely to be robust and less likely to be generalisable compared to large studies".
"As this study was carried out in European men, we do not know whether the findings will apply to homosexuality in women, or even to homosexuality in non-European men. It's really important to appreciate that association does not imply causation," she said.
"All that is required to see a genetic association in this study is for slightly more homosexual men to carry the genetic variant than heterosexual men, and many times this will simply be due to chance."
