1) Diet
Diet is the best natural remedy for autoimmune diseases.  Autoimmune diseases are, for the most part, the product of a poor diet – the Standard American Diet which is SAD.  A low fat vegan (no meat or dairy) diet which includes whole foods and eliminates processed refined foods (including sodas) will cure or arrest these diseases most of the time.

Diet

Many of us have been brainwashed into thinking we have to eat lots of meat and dairy to get enough protein and calcium.  This is totally false and was disproven by a number of thorough studies that were done in the 1950s.  The largest most powerful animals on our planet eat no meat nor dairy.  Consider a horse.  How does it find the calcium and protein it needs to build such a massive powerful body?  It comes only from plant food.  All that protien comes only from plants.  How about cows, elephants, apes, rhinocerouses, giraffs and buffalo?  Eating too much protein causes many undesirable diseases including autoimmune diseases.

2) Tulsi Tea
For 5000 years and to this day, Indian Ayurvedic medicine has revered Tulsi (holy basil) as the "Incomparable One" and the pinnical of herbal medicine.  It is especially good as an immune system modulator.  
 
3) Sasparilla
Home remedy for Autoimmune Diseases:  You may not have to rely on conventional anti-inflammatory as there are natural ones instead.  One such anti-inflammatory is the herb Sarsaparilla.  Sarsaparilla can help with soothing inflamed joints and muscles.
 
The use of herbs can be wonderful help in the treatment of Autoimmune Diseases.  Yarrow is an example of an herb that is a useful remedy.  The use of Yarrow can help to detoxify and cleanse the bloodstream.
 
If you experience muscular pains and/or stiffness; The Yucca herb can help to relieve these symptoms.  It is also effective in treating skin disorders.
 
To help treat Autoimmune Diseases, there are herbs, spices, and vegetables that you may have in your own kitchen that could provide relief from certain Autoimmune Disease symptoms.  Ginger and turmeric are two examples of something you may already have in your kitchen and could provide effective natural home remedy for Autoimmune Diseases.