One of the main differences is over 'liberalism' vs. 'fundamentalism.' As many denominations accepted modern ideas about the Bible, God, and Christ, groups dropped out and formed either new denominations or independent churches that held to traditional views. The issues involved include, for instance, whether Jesus was born of a virgin, whether miracles like the resurrection really happened, whether God created the universe in 6 literal days and whether the Bible is without error. The biggest issue, however, is how to be saved. The liberal view is that salvation is just following the example of Christ to the best of our ability. This view also does not hold to eternal punishment for the lost. Conservatives/fundamentalists hold that mankind is lost in sin and condemned by God and must accept the solution that God provides: Jesus Christ's death on the cross. In this view, which takes the Bible literally, Christ was crucified as a substitute for the punishment we deserve and we only need to trust Him for salvation from our sins. Check out John 3:16, 36; 5:24; Romans 3:10, 23; 4:5; 6:23; 10:9-11; Acts 16:31 and 1 Peter 2:24; 3:18, for instance. I hold this view myself.
Church government is another big difference. Presbyterians hold to multiple Pastor/Elders (synonymous) governing each church where Baptist churches generally have one Pastor who is the sole authority. Methodist churches have an administrative board in each church and churches formed into conferences. Most denominations have some sort of centralized authority structure over local churches but independents reject this. Some local churches are congregational, that is the whole congregation votes on major decisions, where others hold that the Elders make the decisions.
Mode of baptism is an issue between pretty much all Baptist groups, who immerse, and other denominations which sprinkle or pour. Another issue in baptism is whether infants should be baptized and later confirmed when at the age of accountability (as in Catholicism) or whether only accountable believers should be baptized.
Another huge issue today is the exercise of charismatic gifts like speaking in tongues and healing. Many hold that these were for the establishment of the church only and not to be exercised now. Even among the denominations holding to modern exercise of charismatic gifts there are many differences.
Some other differences are whether we have free will or whether God chose who would be saved, whether Christ will return literally and set up a literal thousand-year reign on earth or whether we are in a spiritual millennium now, whether the Bible is to be taken basically literally or whether is can be spiritualized on certain issues. As I said, there are too many differences to address easily but these are some of the most typical.
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