FIFA is investigating claims that Mexico fans chanted anti-gay slurs during its opening match against Cameroon.
FIFA says "disciplinary proceedings were opened against Mexico for improper conduct of spectators" last Friday in Natal.
The same chants were heard during the television broadcast of Mexico's second match against Brazil in Fortaleza on Tuesday.
FIFA President Sepp Blatter and Brazil state president Dilma Rousseff have pledged to use the World Cup as a platform to fight racism and discrimination.
Fare, the European fan monitoring group, has also alerted FIFA to far-right banners displayed by Croatia and Russia fans inside stadiums.
FIFA says only one disciplinary case had been opened by early Thursday.