Under cold running water, thoroughly wash beets. Cut stems leaving 1" of stem and all of the root attached. Place beets into a large pot and fill with COLD water enough to cover beets by 1". Bring to a boil over high heat, then reduce heat to a simmer and cook covered until beets are fork tender. (20-30 minutes).
Drain beets saving liquid in a separate container and immediately plunge hot beets into an ice water bath to stop cooking process. When cool enough to handle, remove skin, stems and roots.
Slice onion into 1/4" thick, separated rings.
Make a cheesecloth spice bag containing cloves and cinnamon stick. In a medium pot combine 1 1/2 Cups of reserved beet cooking liquid, vinegar, sugar, salt and add the spice bag. Bring mixture to a boil, then reduce heat and simmer covered for 5 minutes.
Pack hot, sterilized, 1 Litre pickling jars with alternating layers of onion rings and whole beets. Start with onion rings on bottom and end with onion rings on top.
Ladle hot spice liquid through a strainer into beet filled jars leaving 1/4" air space at top. Seal jars and process in a boiling water bath for 10 minutes.
After processing, remove jars, let cool and store in cupboard. Ready in 2 weeks.