According to John 1.18; 3.16 &18 and 1 John 4.9 Jesus is “the only begotten Son” [monogenase]. Begotten means born, it is the word we derive generate and generation from. In the above verses the prefix ‘mono’ is added to the word ‘begotten’.
In newer translations and paraphrases, like the NIV and The Message the composite word is translated “one and only Son” (NIV) and “only Son” (The Message). These versions capture some of the meaning of ‘only begotten’ or ‘only born’ [monogenase], but they do not communicate the idea of being born which is essential to the word.
The difficulty with translating the word ‘only born’ is the fact that in our western culture one would immediately think of Jesus’ birth in Bethlehem, which is not the primary meaning. Acts 13.30-34 states, “But God raised Him from the dead… And we preach to you the good news of the promise made to the fathers, that God has fulfilled this promise to our children in that He raised up Jesus, as it is also written in the second Psalm, ‘You are My Son; today i have begotten You.’” Clearly, the fact of Jesus being the “only born Son” is based on His resurrection not His incarnation.
In the context of John 3, Nicodemus has come to Jesus to ask about how to obtain a significant relationship with God. Jesus answered that the way one gains a significant relationship with God is by being born into it (‘born again’ or ‘born from above’). It is the “only born Son” alone who provides an invitation to “whosoever” a new birth. Those who receive this new birth gain the significant relationship with God, and they gain it from the One who gives life from the dead.