“These things I write to you…that you may know how you ought to conduct yourself in the house of God, which is the church of the living God, the pillar and ground of the truth. And without controversy great is the mystery of godliness: God was manifested in the flesh, justified in the Spirit, seen by angels, preached among the Gentiles, believed on in the world, received up in glory.” 1 Timothy 3:14-16
The first part of an answer to the question, “What makes Baptist churches different from other churches?” is the issue of authority. Who has the right to decide how a church ought to operate and how Christians ought to conduct themselves when they gather together? It is immensely helpful that Paul wrote to Timothy, a young pastor in the city of Ephesus, to instruct him in how the church and its leadership ought to function. A couple of observations about this passage will suffice to answer our question.
Paul told Timothy that the instructions contained in his letter were to guide him in the conduct of the church, which he called “the house of 
God.” This title is of utmost importance, for it is to God that the church belongs, rather than to men, so it follows that God alone has the right to decide how a church is to be run. The church is not to be self-governed, nor is it to be governed by any body of men who would propose to define its structure and purpose. The NT church is the household of God, an assembly belonging to the living God, and as such it is submit to his authority alone. Any exercise of decision-making in the congregation must be according to the methods and structures proscribed by God for his church and thus exclude any outsider from interfering in the obedience of a local congregation to its head, who is God.
Paul described the church using two construction metaphors; it is the “pillar and ground of the truth.” Both of these images convey essentially the same concept – that the church’s purpose is to support and promote the truth. The church is the foundation or support on which the truth rests, so that it is the truth itself rather than the church which is most important. In other words, the church is to be subject to and guided by the truth as it stands in support of it. And what is this truth which the church is called to support and herald? Paul continues in the next verse with a hymn of exaltation to God.
God himself was made flesh, that is, he became a man, yet his deity was affirmed by the Spirit who performed great miracles through Jesus Christ, culminating in his bodily resurrection from the dead. He was exalted before the angels in heaven and proclaimed before the nations of earth. The true preaching of Christ produces faith in the hearts of its hearers for the One who is even now seated at the right hand of the throne of God in heaven. The truth which the church is called to support and proclaim is nothing other than the gospel of Jesus Christ, so that we can confidently say that the church’s authority is the Savior, who has given instruction through the NT Scriptures to govern and direct his followers. The first part of our answer, then, is Baptists believe that the NT is our final authority in matters of doctrine and practice.