Fruit causes a painful affliction (5)
I believe the answer is:
acorn
'fruit' is the definition.
(acorn is a kind of fruit)
'a painful affliction' is the wordplay.
'painful affliction' becomes 'corn' (I've seen this before).
'a'+'corn'='ACORN'
'causes' is the link.
(Other definitions for acorn that I've seen before include "Oak seed" , "oak's fruit" , "Fruit of the oak tree" , "From which a "tall oak" may grow" , "From which a mighty oak may grow?" .)