Joh 3:1
3:1 There {1} was a man of the Pharisees, named Nicodemus, a {a}
    ruler of the Jews:

 (1) There are none sometimes more unlearned than the learned,
     but the learned as well as the unlearned must desire wisdom
     from Christ only.
     (a) A man of great estimation and a ruler amongst the Jews.

Joh 3:2
3:2 The same came to Jesus by night, and said unto him, Rabbi,
    we know that thou art a {b} teacher come from God: for no
    man can do these miracles that thou doest, {c} except God be
    with him.

    (b) We know that you are sent from God to teach us.
    (c) But he in whom some part of the excellency of God
        appears.  And if Nicodemus had rightly known Christ, he
        would not only have said that God was with him, but in
        him, as Paul does in 2Co 1:19.

Joh 3:3
3:3 {2} Jesus answered and said unto him, Verily, verily, I say
    unto thee, Except a man be born again, he cannot {d} see the
    {e} kingdom of God.

 (2) The beginning of Christianity consists in this, that we
     know ourselves not only to be corrupt in part, but to be
     wholly dead in sin: so that our nature has need to be
     created anew, with regard to its qualities, which can be
     done by no other power, but by the divine and heavenly, by
     which we were first created.
     (d) That is, "go in", or "enter", as he expounds himself
         below in Joh 3:5.
     (e) The Church: for Christ shows here how we come to be
         citizens and to have anything to do in the city of God.

Joh 3:4
3:4 Nicodemus saith unto him, How {f} can a man be born when he
    is old?  can he enter the second time into his mother's
    womb, and be born?

    (f) How can I who am old be born again?  For Nicodemus
        answers as if Christ's words were only addressed to
        himself.

Joh 3:6
3:6 That which is born of the flesh is {g} flesh; and that which
    is born of the Spirit is spirit.

    (g) That is, fleshly, namely, wholly unclean and under the
        wrath of God: and therefore this word "flesh" signifies
        the corrupt nature of man: contrary to which is the
        Spirit, that is, the man ingrafted into Christ through
        the grace of the Holy Spirit, whose nature is
        everlasting and immortal, though the strife of the flesh
        remains.

Joh 3:8
3:8 The wind bloweth where it {h} listeth, and thou hearest the
    sound thereof, but canst not tell whence it cometh, and
    whither it goeth: so is every one that is born of the
    Spirit.

    (h) With free and wandering blasts as it wishes.

Joh 3:9
3:9 {3} Nicodemus answered and said unto him, How can these
    things be?

 (3) The secret mystery of our regeneration which cannot be
     comprehended by man's capacity, is perceived by faith, and
     that in Christ only, because he is both God on earth, and
     man in heaven, that is to say, man in such a way that he is
     God also, and therefore almighty: and God in such a way
     that he is man also, and therefore his power is made
     manifest to us.

Joh 3:11
3:11 Verily, verily, I say unto thee, We speak that we do know,
     and testify that we have seen; and ye receive not our {i}
     witness.

     (i) You handle doubtful things even though you have no
         solid basis for believing them, and yet men believe
         you: but I teach those things that are of a truth and
         well known, and you do not believe me.

Joh 3:13
3:13 And no {k} man {l} hath ascended up to heaven, but he that
     came down from heaven, [even] {m} the Son of man which {n}
     is in heaven.

     (k) Only Christ can teach us heavenly things, for no man
         ascends, etc.
     (l) That is, has any spiritual light and understanding, or
         ever had any, but only the Son of God who came down to
         us.
     (m) Whereas he is said to have come down from heaven, this
         must be understood as referring to his Godhead, and of
         the manner of his conception: for Christ's birth upon
         the earth was heavenly and not earthly, for he was
         conceived by the Holy Spirit.
     (n) That which is proper to the divinity of Christ, is here
         spoken of the whole Christ, to show us that he is but
         one person in which two natures are united.

Joh 3:16
3:16 {5} For God so loved the world, that he gave his only
     begotten Son, that whosoever believeth {o} in him should
     not perish, but have everlasting life.

 (5) Nothing else but the free love of the Father is the
     beginning of our salvation, and Christ is he in whom our
     righteousness and salvation dwells: and faith is the
     instrument or means by which we apprehend it, and
     everlasting life is that which is set before us to
     apprehend.
     (o) It is not the same to believe in a thing, and to
         believe about a thing, for we may not believe in anything
         except in God alone, but we may believe about anything
         whatever, says Nazianzene in his Oration of the Spirit.

Joh 3:17
3:17 {6} For God sent not his Son into the world {p} to condemn
     the world; but that the {q} world through him might be
     saved.

 (6) Christ does not condemn, but rather despising Christ
     condemns.
     (p) That is, to be the cause of the condemning of the
         world, for indeed sins are the cause of death;
         however, Christ will still judge the living and the
         dead.
     (q) Not only the people of the Jews, but whoever will
         believe in him.

Joh 3:19
3:19 {7} And this is the {r} condemnation, that light is come
     into the world, and men loved darkness rather than light,
     because their deeds were evil.

 (7) The only reason why men refuse the light that is offered to
     them is wickedness.
     (r) That is, the cause of condemnation, which remains in
         men, unless through God's great benefit they are
         delivered from it.

Joh 3:21
3:21 But he that {s} doeth truth cometh to the light, that his
     deeds may be made manifest, that they are wrought {t} in
     God.

     (s) That is, he that leads an honest life, and is void of
         all cunning and deceit.
     (t) That is, with God, God as it were going before.

Joh 3:25
3:25 {8} Then there arose a question between [some] of John's
     disciples and the Jews about purifying.

 (8) Satan inflames the disciples of John with a fond emulation
     of their master in order to hinder the course of the
     gospel: but John, being mindful of his office, not
     only puts a stop to their endeavours, but also takes
     occasion by that means to give testimony of Christ, that in
     him alone the Father has set forth everlasting life.

Joh 3:27
3:27 John answered and said, A man {u} can receive nothing,
     except it be given him from heaven.

     (u) Why are you trying to better my state?  This is every
         man's lot and portion, that he cannot better himself in
         the slightest way.

Joh 3:31
3:31 He that cometh from above is above all: he that is of the
     earth is {x} earthly, and {y} speaketh of the earth: he
     that cometh from heaven is above all.

     (x) Is nothing else but man, a piece of work made of the
         slime of the earth.
     (y) Is characterized by nothing but corruption, ignorance,
         dulness, etc.

Joh 3:32
3:32 And what he hath {z} seen and heard, that he testifieth;
     and {a} no man receiveth his testimony.

     (z) What he knows fully and perfectly.
     (a) That is, very few.

Joh 3:35
3:35 The Father loveth the Son, and hath {b} given all things
     into his hand.

     (b) Committed them to his power and will.

Joh 3:36
3:36 He that believeth on the Son hath everlasting life: and he
     that believeth not the Son shall not {c} see life; but the
     wrath of God abideth on him.

     (c) Shall not enjoy.