“It is necessary to cut the misconception of thinking that it is enough to take refuge once in awhile. You should take refuge again and again, both day and night.” — Guru Rinpoche
The ultimate protector practice in Buddhism is Taking Refuge in the Three Jewels. We take refuge in the Buddha, Dharma and Sangha for three key reasons, according to the great Theravadan teacher Bhikkhu Bodhi: “the dangers pertaining to the present life; the dangers pertaining to future lives; the dangers pertaining to the general course of existence.” In short — danger. Practicing Dharma can help free us from fears. When you understand the true nature of existence, and the true source of fear — that of clinging to our egos — all dangers suddenly seem harmless.
The practice of the “Buddha’s teaching starts with taking refuge, wrote Bhikkhu Bodhi.  We always take refuge in the Three Jewels as a base:
Buddham saranam gacchami
I go for refuge to the Buddha;
Dhammam saranam gacchami
I go for refuge to the Dhamma;
Sangham saranam gacchami
I go for refuge to the Sangha.
In Vajrayana Buddhism, we additionally take refuge in the Inner Jewels of Refuge: Guru, Yidams and Dakinis.
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Padmasambhava: Karmic Obscurations are Brought to an End
The great Buddha Padmasambhava, Guru Rinpoche, taught: “Having taken refuge in the Three Jewels, you are called a Buddhist. Without having taken refuge, you are not included among the Buddhist group, even though you may claim to be a holy person, a great meditator, or the Buddha in person.” 
This was the first “good quality” Padmasambhava outlined in his teaching to Lady Tsogyal, on the “eight good qualities of taking refuge.” The eight qualities — which assume you have great faith and perfect practice of Refuge — are, in the Buddha Padmasambhava’s words:
- “You are called a Buddhist.”
- “Taking refuge is known as that which causes you to become a suitable basis for all types of vows.”
- “When a genuine feeling of taking refuge has arisen, karmic obscurations are utterly brought to an end.”
- “You will possess vast merit. The mundane merits of long life, good health, splendor, and majestic dignity, great wealth and so forth, result from taking refuge.”
- “You will be immune to attack by humans and non humans, and immune to the obstacles of this life.”
- “When genuine taking refuge has arisen in your being, it is impossible not to accomplish whatever you intend.”
- “You will not fall into evil destines or perverted paths.”
- “The final benefit is that of swiftly attaining true and complete enlightenment.”
“How is One Protected by Having Taken Refuge?”
When Lady Tsogyal asked great Padmasambhava to explain how one is protected by refuge, he answered:
“Whoever practices the trainings correctly, having taken the refuge as explained, will definitely be protected by the Three Jewels… You will definitely also be protected from the fears of this life.”
The great teacher explained that the ultimate refuge is the Dharma: “You may then argue, if one is protected by taking refuge in such a way, does it mean that the Buddhas appear and lead all sentient beings? The reply is that the Buddhas cannot take all sentient beings out of samsara with their hands. If they were able to do that, the Buddhas with their great compassion and skillful means would have already freed all beings without a single exception.
“Well then, you may ask, how is one protected? The answer is that one is protected by the Dharma. When taking refuge has arisen in your being, you do not need to practice other teachings. It is impossible that you will not be protected by the compassion of the Three Jewels.”
What the Teachers Say about Taking Refuge:
The Method of Taking the Refuge Vow
A Buddhist takes Refuge daily, and throughout the day. At some point, the Buddhist will typically make an initial vow in front of his teacher — at least in Vajrayana schools.
When Lady Tsogyal asked the Nirmanakaya master Padmakara: “What is the method of taking the refuge vow?” the great master replied that in addition to prostrating and circumambulating one’s teacher, and presenting him with offerings, one should state the vow, out loud:
“Master, please listen to me. Buddhas and Bodhisattvas in the ten directions, please listen to me. From this very moment until attaining supreme enlightenment, I, (your name), take refuge in the Supreme of all humans, the truly perfected Dharmakaya Buddhas.
“I take refuge in the Supreme of all peace, devoid of attachment, the Dharma of Mahayana.
“I take refuge in the Supreme of all assemblies, the Sangha of noble Bodhisattvas who are beyond falling back.”
After repeating three times, the vow is taken. Usually, this vow, is included in most formal empowerments and initiations.
 “Going for Refuge & Taking the Precepts” by Bhikkhu Bodhi 1994
 Dakini Teachings, Padmasambhava’s Oral Instructions to Lady Tsogyal, Chapter “Taking Refuge 592