Breakfast passes through one end of the stomach into parts of the ileum (6)
I believe the answer is:
muesli
'breakfast' is the definition.
(I've seen this before)
'stomach into parts of the ileum' is the wordplay.
'stomach' becomes 's' (this might be a standard abbreviation which I don't know about).
'into' means one lot of letters goes inside another.
'parts of' is an anagram indicator.
'ileum' with letters rearranged gives 'mueli'.
's' placed inside 'mueli' is 'MUESLI'.
'passes through one end of the' is the link.
This may not be correct. Some or all of it may be part of another bit of the clue.
Can you help me to learn more?
(Other definitions for muesli that I've seen before include "Type of breakfast cereal" , "Mixture of untoasted dry cereals and fruits" , "healthy breakfast?" , "Mixture of crushed grain, nuts etc" , "Mixture of cereals etc" .)