I had pain, ultimately, in vital organ (6)
I believe the answer is:
kidney
'organ' is the definition.
(kidney is a kind of organ)
'i had pain ultimately in vital' is the wordplay.
'i had' becomes 'id' (I'd).
'ultimately' says to take the final letters.
'in' indicates putting letters inside.
'vital' becomes 'key' (I've seen this before).
The last letter of 'pain' is 'n'.
'id'+'n'='idn'
'idn' put inside 'key' is 'KIDNEY'.
(Other definitions for kidney that I've seen before include "Internal organ producing urine" , "Character" , "Bodily organ" , "body part" , "Renal organ" .)