Dear Diego.

you would better to check the procedure: first transfer the tissue from mouse to formaldehyde (10%) solution (for not more than 12 hrs) then transfer it to ethanol (50%)(1 hr), then --> ethanol 70% (you can stop the process in this step and continue the procedure after any time, 70% ethanol solution is suitable for leaving the sample for a long time even for many months). when you decided to continue your experiment, transfer the sample form 70% ethanol to --> ethanol 90% (1 hr) --> absolute ethanol (container 1) (30 mins) --> absolute ethanol (container 2) (30 mins) --> xylene solution (container 1) (30 mins)--> xylene solution (container 2)(30 mins) --> and then --> paraffin bath (container 1) --> paraffin bath (container 2) --> paraffin block and then pouring melted paraffin in the block. note that the temperature of paraffin bath should not exceed 60˚ C.

keep containers contents fresh. especially for absolute ethanol and xylene.

Note that if you can not dehydrate the sample completely by ethanol series, then you can not remove the fats from the sample by xylene and consequently paraffin would not penetrate to the sample correctly.

REGARDS

I concur with the previous responses.  You most likely have a processing problem, probably insufficient dehydration of tissue and subsequent clearing with xylene and infiltration with paraffin.  This is imperative to solve before you can move forward.  Good luck.  There are lots of histology texts to guide you in choosing an appropriate processing schedule.