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Indeed, autoimmune type diseases can lead to dry eyes. If your main problem is dryness in the morning, it may be that your eyelids don't close tight while you are sleeping. Sometimes, I will suggest to patients that they instill some artificial tear ointments in the eyes right before going to sleep. This will protect your eyes better while you are sleeping. Also, if you can, humidify the air and turn off ceiling fans at night.
If artificial tears and the above don't help, the next step to treating dry eyes is to insert plugs into the tear drainage ducts. There is an eyedrop called Restasis that may also help you in this condition. Finally, people are starting to use autologous serum drops (made from your own blood).
Hope this helps and thank you.