The commonly accepted story for the origin of the pretzel begins around A.D. 610, when Italian monks presented their young students with treats of baked dough twisted in the shape of crossed arms (then a common prayer posture). They called them “pretiolas” or “little rewards,” and were a reward for children who had memorized their prayers.
An alternate explanation for the word pretzel is that they were originally called “bracellae,” the Latin term for “little arms,” from which Germans later derived the word “bretzel.”
As the custom spread through medieval Europe, the pretzel’s three holes came to represent the Holy Trinity—Father, Son and Holy Spirit—and the twisty baked good became associated with good luck, long life and as a way of providing them with both spiritual and literal sustenance.
Pretzels, made of a simple mixture of water, flour and salt, were an ideal food to consume during Lent, when all types of meat, dairy and eggs were prohibited. By the 16th century, it had become popular tradition to eat pretzels on Good Friday in Germany, and Catholics once considered them the “official food of lent.”
To this day here are still many Catholic traditions surrounding the pretzel. Via wikipedia:
In southern Germany and adjoining German-speaking areas, pretzels have retained their original religious meanings and are still used in various traditions and festivals.
In some areas, on January 1, people give each other lightly sweetened yeast pretzels for good luck and good fortune. Sometimes children visit their godparents to fetch their New Years pretzel. Especially Catholic areas, such as Austria, Bavaria or some parts of Swabia, the “Palm pretzel” is made for Palm Sunday celebrations. An old tradition on Palm Sunday dating back to 1533 is the outdoor pretzel market (Brezgenmarkt) in the Hungerbrunnen Valley near Heldenfingen.
On Laetare Sunday in Luxembourg, the fourth Sunday in Lent, there is a festival called “Pretzel Sunday”. Boys give their girlfriends pretzels or cakes in pretzel form. The size symbolizes how much he likes her. In return, if a girl wants to increase his attention, she will give him a decorated egg on Easter. The pretzel custom is reversed on Pretzel Sunday during leap years.
Popular during Lent in Biberach are “Lent pretzels”, which are shortly boiled in water before baking and afterwards sprinkled with salt.