One among three long-standing mystery diseases listed in Wikipedia is acute encephalitis syndrome (AES) in Muzaffarpur, Bihar. This disease has remained for over two decades without determining a cause for; hence it is called mystery disease. It occurs annual seasonal outbreaks during the months of April-July, affecting hundreds of children with 40-60% mortality, according to local physicians.
Original Source [2]
Links:
[1] http://admin.indiaenvironmentportal.org.in/feature-article/acute-encephalitis-syndrome-children-muzaffarpur-hypothesis-toxic-origin
[2] http://www.currentscience.ac.in/Volumes/106/09/1184.pdf
[3] http://admin.indiaenvironmentportal.org.in/category/author/t-jacob-john-0
[4] http://admin.indiaenvironmentportal.org.in/category/author/mukul-das
[5] http://admin.indiaenvironmentportal.org.in/category/journal/current-science
[6] http://admin.indiaenvironmentportal.org.in/category/thesaurus/encephalitis
[7] http://admin.indiaenvironmentportal.org.in/category/thesaurus/child-health
[8] http://admin.indiaenvironmentportal.org.in/category/thesaurus/muzaffarpur-d
[9] http://admin.indiaenvironmentportal.org.in/category/thesaurus/uttar-pradesh