Besides Nagaraja, there are sanctums for Lord Siva and Ananthakrishna too. Images of Jain Tirthankaras, Mahavira and Parswanatha are seen carved on the pillars of the temple. The entrance of the temple is reminiscent of Chinese architecture of Buddha Vihara.
From the five headed-serpent deity of the temple, the name of this place (town) Nagercoil is derived and gradually it's old name Kottar has mostly faded. Still there is a part of the town that was called Kottar and hence the old name still remains.
It is difficult indeed to ascertain the exact age of the temple. There is no authentic epigraph to aid this historian under the topic of Chronology. The Mountain Mahendragiri in the district of Kanyakumari is referred to as the abode of Nagas in the Ramayana of Valmiki. From this fact it can be presumed that the origin of Naga influence in the area goes back to legendary times.
There is a traditional background regarding the origin of Nagaraja temple.
One day when a girl was cutting grass, blood began to spurt from below. Soon she discovered that the sickle had cut into the head of a five-headed serpent. Dazed with fear the girl fled to the nearest village and reported what she had seen. People in large numbers flocked to the spot and witnessed the miracle with their own eyes. By the joint effort of the villagers, the place was cleared and preserved for the purpose of worship.
They built a small shrine in the locality and worshipped the five-headed serpent. Hearing that the miracle happenend at this place people from different places used to visit the temple and offer poojas.
Once the King of Kalakkad who was stricken with leprosy came to the temple on Sunday in the Tamil Month of Avani and did penance before the deity. Miraculously, the king got cured of the deadly disease and the fame of the temple spread far and wide. The king in gratitude built the present temple and on every Sunday during the month of Avani (August/September) the king, accompanied by his wife and children, used to visit the temple and offer poojas. Ever since, the temple is visited on every Sunday in the month of Avani by thousands of devotees and the serpent shrine is worshipped.