This timeline focuses on the events of the Elfen Lied manga series. However, with the exception of events at or near the conclusion of the anime, it may be assumed events mesh up between the two versions fairly well.
1000 Years Prior -
A family living in Japan's Kanto Region begins to produce children with vestigial horns protruding from their heads, leading the superstitious folk of that time to believe they are cursed.
700 to 800 years prior -
The Original Diclonii are hunted, killed and persecuted by non-horned Japanese, presumably in Kamakura area. They flee to the island that will eventually house the Diclonius Research Institute, specifically to the underground grotto, which actually worsens their mutations due to radioactivity. The family eventually gains a resistance to radiation, and takes the name given to the lands in which they dwell--Kakuzawa, meaning 'Valley Of The Horns.'
Intervening 500 to 600 years -
The Kakuzawas obtain wealth and prominence, and begin to throw off the shame of their horns by crafting racial myths about the supposed power their ancestors wielded, including a eugenics-based one that says intermarriage with 'humans' has diluted their bloodline, which will eventually be awoken and purified by a messianic figure.
60 to 70 years prior -
The man who will become known as Chief Kakuzawa is born, steeped in the traditions and myths his family has been raised with, and intent on using modern technology to bring about the dominance of his 'kind'.