Chapter 18.4

iv. True believers may have the assurance of their salvation divers ways shaken, diminished, and intermitted; as, by negligence in preserving of it; by falling into some special sin, which woundeth the conscience, and grieveth the Spirit; by some sudden or vehement temptation; by God's withdrawing the light of his countenance and suffering even such as fear him to walk in darkness and to have no light: yet are they never utterly destitute of that seed of God, and life of faith, that love of Christ and the brethren, that sincerity of heart and conscience of duty, out of which, by the operation of the Spirit, this assurance may in due time be revived, and by the which, in the meantime, they are supported from utter despair. 
After giving a strong affirmation of the believer's "infallible assurance of faith"--and of the many blessings that the Spirit bestows when we are secure in our salvation--the Confession introduces a typical dose of realism. It is not easy to have the assurance of our salvation; indeed, for many Christians it is a lifelong struggle.

Spiritual doubts have many causes; there is more than one way for the assurance of our salvation to be "shaken, diminished, and intermitted." Sometimes we simply fail to fulfill our biblical duty to make our calling and election sure, and as a result we may waver in the confidence of our salvation. 

There are also times when we fall into serious sin, which grieves the Spirit of God within us. It is hardly surprising that unconfessed transgression diminishes our sense of peace with God. When we lack the assurance of their faith, therefore, we should examine our conscience and consider whether we have any sins to confess.

A lack of assurance is not always the result of moral failure, however. Sometimes we are afflicted by a strong and sudden temptation that leads us to doubt our salvation. There are also times--and this is a great mystery--when God withdraws from us (so to speak), leaving us without an intimate sense of his presence. This is an experience that David sometimes endured, as well as Job, and even our Lord himself, when he suffered his Father's absence on the cross.  

The important thing to know is that these struggles are all normal for the Christian life. The people the Confession identifies as lacking the full assurance of their faith are true believers.  

Dr. Philip Ryken is the president of Wheaton College and the author of numerous books, the most recent of which is Loving the Way Jesus Loves (Crossway, 2012).