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Well, as of "The Pilot"...

When the Doctor has companions with him when he regenerates, they generally continue to travel with him, although it may take them time to get used to his new incarnation.

  • Ben Jackson & Polly Wright were with the First Doctor when he regenerated (at the end of "The Tenth Planet") & remained with the Second Doctor.
  • Sarah Jane Smith was with the Third Doctor when he regenerated (at the end of "Planet of the Spiders") & remained with the Fourth Doctor.
  • Adric, Tegan Jovanka & Nyssa of Traken were with the Fourth Doctor when he regenerated (at the end of "Logopolis") & remained with the Fifth Doctor.
  • Peri Brown was with the Fifth Doctor when he regenerated (at the end of "The Caves of Androzani") & remained with the Sixth Doctor.
  • Rose Tyler was with the Ninth Doctor when he regenerated (at the end of "The Parting of the Ways") & remained with the Tenth Doctor.
  • Clara Oswald was with the Eleventh Doctor when he regenerated (at the end of "The Time of the Doctor") & remained with the Twelfth Doctor.

There were also some regeneration that no companions witnessed:

  • When the Second Doctor was forced to regenerate in "The War Games", Zoe Heriot & Jamie McCrimmon had already been sent back home by the Time Lords.
  • When the Sixth Doctor regenerated in "Time and the Rani", Mel was unconscious.
  • When the Seventh Doctor regenerated in "Doctor Who", he was travelling alone at the time.
  • When the Eighth Doctor regenerated in "The Night of the Doctor", Cass was dead.
  • When the War Doctor regenerated in "The Day of the Doctor", he was travelling alone at the time.
  • When the Tenth Doctor regenerated in "The End of Time", he was travelling alone at the time.

Additionally, some companions like Mel, River Song, and Sarah Jane met more than one Doctor without actually witnessing the regeneration.

Finally, here's an oddity. Donna, Rose and Captain Jack were present for the Tenth Doctors aborted regeneration at the end of "The Stolen Earth". They all stayed with him for the rest of that story, but then never met him again after it.