Chapter 13.2

ii. This sanctification is throughout, in the whole man; yet imperfect in this life, there abiding still some remnants of corruption in every part; whence ariseth a continual and irreconcilable war, the flesh lusting against the Spirit, and the Spirit against the flesh. 

The first section of Chapter 13 makes strong claims about the efficacy of the Spirit's sanctifying work. Believers "are sanctified," the Confession says, "really and personally." The dominion of sin "is destroyed;" the lusts of the flesh "are more and more weakened and mortified;" and so on.  Thus we can have absolute confidence that God will do his sanctifying work in our lives.  

Similarly, the second section begins with the bold assertion that the Holy Spirit sanctifies the whole person. When God's indwelling Spirit makes us more and more holy, this affects every aspect of life: body and soul, heart and mind. Because the Spirit is holy, the believer's whole life is transformed and purified. 

Left by themselves, without any further qualification, these confident claims might give the wrong impression that believers always make constant progress in holiness, or that we never experience any spiritual setbacks. Few things could be farther from the truth. Ever realistic about the real struggles of the Christian life--and careful to provide sound pastoral guidance--the Westminster Divines are honest about the life and death struggle that sanctification requires.

Sanctification is never perfect in this life, but always imperfect. Here the Confession takes a clear and obvious stand against the perfectionism of some evangelical traditions. We cannot completely escape the corruption of sin. Not even one single area of life will ever be totally free from sin.

As a result, we are engaged in constant spiritual warfare. As Paul explains in Romans 8, the flesh is always fighting against the Spirit, and the Spirit is perpetually waging war against the flesh.  

All of this helps us to have the right expectations for our spiritual experience. God has promised that over time we will make progress in holiness. But sin will be a struggle for us right to the end of our lives.