The cave of punarjani, near Vilwadrinatha temple, is a wonderful phenomenon. Its location is towards the east of the temple at a distance of more than two kilometers.

The three rocky hills "Bhoothamala", "Vilwamala" and "Moorikkunnu" which stretch out in the east-west direction on the southern bank of Bharathappuzha are known as "Vilwamala" as a whole. The "punarjani" cave is in between the Vilwamala and the Bhoothamala. It is believed that the punarjani cave was built by "Viswakarma" having been ordered by "Devendra", as per the request of Parasurama for the salvation of spirits of dead people, who were already purified by the sight of Vilwadrinatha (the idol in the eastern shrine). Before starting to Punarjani we have to touch the "Ganapathi theertham" (which never gets dried up) on the northern side of the mountain about quarter of a mile eastwards from the temple.

Next we can reach a steep rock about seventy feet high on travelling about one and a half miles over the mountain. The broad "Papanasini Theertha" is seen if we proceed a little further in the southwest direction over the narrow projection on the rock. This was made by Parasurama and the presence of Ganga has been brought in this Theertha. Railings have been provided here for the devotees to walk easily without fear of falling down from the narrow projection of the rock.

The Entrance of Punarjani cave can be seen at a height of about six feet when we reach at the bottom of the steep rock after purifying our body by a dip in the papnasini theertha. Entering the cave we can walk a little towards the north bending the body. Then we have to move in the northwest direction in the sitting posture inside the cave. The only relief in the darkness is the streaks of light comming through the crevices of the rock. After that we have to cover some distance lying flat on the back and moving towards the east in that position touching the overhanging rock. Covering some distance in utter darkness in which even the person preceeding or following cannot be seen, a place can be reached where we have to lie over our belly. The divinity of the cave is based on the path beyond this. Any person, fat or lean, has to continue his movement upwards with' another's help (touching the feet of the one who preceeds) through a hole, which has only a diameter of about one foot, in the absence of breathing air. Then we have to creep over our belly along a broad slope, which ends in a square place of sides about twelve inches and then reach the exit. Once we enter the Punarjani cave it takes about three-quarters of an hour to reach the exit.

The custom is to go to papanasini again to purify the body and then go to the entrance once again. Next the devotees have to bathe or wash their hands, feet and face in the "Pathala Theertha" on the west at a distance of about thirty feet. It is believed that Parasurama who had brought the presence of the purified water of "Brahmakamandalu" here made this also. The next step is to take holy water in our hands from the "Kombutheertha", which was formed when Indra's elephant Iravatha struck his tusk on the rock. Nearby lies the "Ambutheertha" from which water has to be taken out using some stick or anything like that. People believe that one "Janma" or span of life is reduced from the cycle of births and deaths if we go through the punarjani cave once. The "Punarjani noozhal" (going through the cave) is done only once in a year on the day of Guruvayoor Ekadasi, which comes before the full moon day in the malayalam month of Vrischikam (Nov - Dec). On that day several people take part in this sacred attempt from morning till evening.

When the temple was rebuilt in the year ME 1055(Malayalam Era) after the fire accident, an opening as that of a cave was noticed in front of the western shrine. Eventhough some people went down the steps and tried to explore the cave the attempt was dropped because of the unending number of steps and the horrifying darkness inside. The cave was closed using 'granite slabs leaving a small hole in the stone slab to identify the spot. The granite slab seen with a small hole near the pathway of "Padinjarambalam" gives a clue to this. The Vilwampurana says that there is a 'Vilwa tree' in golden yellow colour under the western shrine and the fruits of this tree can liberate people from recurring births and deaths. Thiruvilwamala derives its name from this sacred tree. It is also said that the pathway inside the cave seen near the peepul tree close to the eastern gateway of the temple had been connected to 'Tirunelli' through an underground passage. The story goes that when a priest returning through this passage after worshipping the deity at Tirunelli, the young lady walking in front showing light to the priest got impure and consequently the underground passage behind was sealed forever. Even now a part of this underground passage where extreme darkness prevails is explorable.

The humming sound heard through the cracked wall of the "Saraswathikundu" and the disappearance of any small object put through the small hole in the Padinjarambalam evidently prove the existence of a cave under the temple. Years ago, water for "Abhishekam" (bathing the deity) in the western shrine used to spring up through a small hole in front of the idol. It is also seen closed at present due to unknown reasons. There are a lot of legends about 'Moorikkunnu', 'Thalavettipara', 'Monnuruttikallu', 'Maharshipala', etc. which are only just mentioned .