Though challenges abound across the world, there are several types that stand out. The Vatican's envoy to a European conference in late 2012 highlighted the nature of these challenges.
MSGR. DOMINIQUE MAMBERTI
Secretary for Relations with States (Vatican)
"With the increase of religious intolerance throughout the world, it is well documented that Christians are among those most discriminated against, even within the OSCE region. In fact, in some participating states intolerant and even discriminatory laws, decisions and behavior, which deny this freedom, still exist against the Catholic Church and other Christian communities.”
The first type of persection are in countries or areas where Christians form a minority, and face persecution from other religious groups. Christians at times face death by Muslim groups in countries like Nigeria, or destruction of their worshiping sites, like in Egypt and Indonesia; or by radical Hindi groups in India and Pakistan.
The second type is state sponsored persecution in place like China, where religion is tightly controlled by the state, or Saudi Arabia, who does not recognize the rights of Christians to worship freely. Often times, these countries do not even have diplomatic ties with the Vatican.
The third type, less recognized and much less violent as well, is the perceived social persecution of Christians. It has been characterized recently as a fight for religious freedom. On countries like the United States and the Philippines it takes form in the showdowns over healthcare laws. Or in Europe, over an employees right to wear a cross or to object to registering homosexual unions, are two recent examples.