The Wisconsin Synod teaches that agreement on all the teachings of Scripture is necessary for all forms of fellowship. The Missouri Synod teaches that full agreement is necessary only for altar and pulpit fellowship. Wisconsin teaches that the same scriptural principles apply to all forms of church or religious fellowship. All joint prayer is an expression of fellowship. Missouri teaches that there can be joint prayer that is not an act of fellowship. In practice Missouri also indicates that full agreement is not necessary for worship at occasional joint Christian celebrations, Reformation services, convocations, rallies. Some Missouri pastors allow "ecumenical wedding services" at which pastors or priests outside their fellowship may participate.
Wisconsin practices "close" or "closed" communion, inviting to their altars only those who are members of congregations in WELS fellowship. Although Missouri officially teaches "close(d)" communion, many pastors and churches practice "open" communion, allowing joint communion with those not in doctrinal agreement with the Missouri Synod.
There are also differences in the doctrine of the church and ministry between the two synods. Wisconsin teaches that God has not ordained any particular form of the church. The invisible church is present in the local congregation and the synod. Both can be called church in the same sense. Missouri's official teaching seems to be that the local congregation is the only "divinely appointed" form of the church. By contrast the synod is a human arrangement.
Wisconsin teaches that the pastor of a local congregation is only one form of the divinely instituted public ministry. Other forms are teachers, professors, called administrators, etc. The specific form is determined by the church's call. Missouri seems to teach that the only divinely instituted form of the public ministry is that of pastor of a local congregation. All other positions are auxiliary to this. However, there appears to be a number of different teachings on the church and ministry currently in the Missouri Synod.
According to the WELS, scripture assigns the headship role to men and a helping role to women, only men serve in offices and roles that involve an exercise of authority over other men. Missouri does not allow women to serve as pastors but allows women to serve in a number of areas which involve the exercise of authority over men.