The term "Holy See" is from the Latin Sancta Sedes, meaning “holy chair.” It is said that the Holy See is the jurisdiction in Rome of the Catholic Church. In other words, it is similar to a government, which is not surprising considering that the Vatican is its own country and has its own money and its own laws. However, there is a difference between the Holy See, which dates back to early Christian times, and Vatican City, which came into existence in 1929 with the signing of the Lateran Treaty between the See and the Italian government. The Holy See is an episcopal designation, while Vatican City is primarily a political and diplomatic one.
The government of the Holy See includes tribunals, congregations, pontifical counsels and numerous other bureaucratic entities. Of course the pope is the head of the See, as he is considered the head of the Catholic Church. The secretariat of state is the second in command of the See and oversees the 175 diplomatic worldwide relationships and offices. The See is a member of numerous international organizations, including the United Nations.
From a biblical standpoint, the very existence of a Holy See is problematic on at least two points. First, the concept of a “holy chair” in which resides the head of the church is unscriptural. The true church is never to consider one man as its head, no matter his title. The exalted Head of the true Body of Christ is Jesus Christ, the living Head of the living church. How can the living church be headed by a mortal man who dies? Second, the Bible nowhere gives credence to the idea of the church forming its own city-state or its own government. The church as a political or diplomatic kingdom is unknown in Scripture. In fact, Jesus made it clear that His kingdom is not of this world (John 8:23; 18:36). The Bible never condones or encourages the establishment of earthly kingdoms or diplomatic entities because these things, by their very nature, focus attention on the world, which is passing away (1 Corinthians 7:31; 1 John 2:17). Christians are to be focused on the heavenly kingdom and our only diplomatic efforts are to be spreading the gospel of Jesus Christ and warning others of the wrath to come.