I certainly don’t mean to cast aspersions on anyone’s religious practices, but I do want to caution you about the findings from a new study that will make you think twice about following one particular common custom. The problem: With this custom, worshippers often unknowingly rub bacteria—including the kind found in fecal matter!—on their own faces.

What’s more, as I looked into this matter, I discovered a number of other hazards lurking in our churches and synagogues—toxins, allergens, irritants, germs, etc.—that can undermine the health of unwary worshippers.

To discuss how to stay safe during services, I contacted William Schaffner, MD, professor in the department of preventive medicine and medicine/infectious diseases at Vanderbilt University School of Medicine in Nashville.

Here’s what worshippers should watch out for…

Contaminated holy water. Researchers from the Institute of Hygiene and Applied Immunology at the Medical University of Vienna in Austria tested samples of holy water from 39 churches and shrines in that country. Christian churches use holy water for baptism. In addition, in Catholic churches and certain other denominations, there is a permanent font (basin) at the church entrance. Worshippers dip their fingers into the holy water, then anoint themselves by touching their faces, chests and shoulders to make the sign of the cross.

Study findings: All holy water samples from churches and hospital chapels showed extremely high concentrations of heterotrophic plate counts (used to measure microorganisms such as bacteria, molds and yeasts in water)…frequently visited churches also showed signs of fecal contamination as well as staphylococcus and other bacteria. The likely source was worshippers’ hands. (We can’t be sure that holy water in this country has the same problem, but there’s no reason to assume that it doesn’t.)

Among the waters tested were those from “holy springs,” which are literally springs in the ground from which water flows (like in the famous grotto at Lourdes). The belief that these springs have healing powers is largely a Catholic tradition, but people from all faiths sometimes drink from or bathe in these springs. (The researchers suggested that holy springs acquired their healing reputations because they actually did provide water that was cleaner than the water available in cities and towns centuries ago—but of course, that is no longer the case.) New findings: Only 14% of holy springs met the microbiological and chemical requirements for modern drinking-water regulations. Many springs were contaminated with E. coli and Campylobacter, which can cause severe diarrhea.

Self-defense: If you want to anoint yourself with holy water, dip only a fingertip, then when you touch your face, touch only your forehead—your risk is minimized as long as you avoid your lips and eye area, Dr. Schaffner said. Wash your hands or use a hand sanitizer as soon as possible afterward. Also, ask your priest or church sexton how often the fonts are emptied, cleaned and disinfected—your concern may encourage increased attention to this matter. If you have an infant who is going to be baptized, make certain that the special font used for baptism will be disinfected right before the service. And never drink the water from a holy spring even if you see others doing so.

Communal communion chalices. Most Christian denominations include the sacrament of communion, in which wine and bread are shared—and often worshippers drink from a single large cup called a chalice. When offering wine using a communal chalice, officiants generally wipe the rim with a cloth before serving the next person. This reduces the chances of spreading colds, flu, oral herpes and other viruses—but it certainly doesn’t eliminate the risk.

Safer: Many churches offer the option of receiving communion from tiny individual cups, Dr. Schaffner noted. If your church does not do this, speak to the minister or priest about implementing this practice.

Shared yarmulkes. Most synagogues have a basket of the traditional head coverings for men who forget to bring their own. But just as schoolchildren are at risk for catching head lice when they share hats, there is a chance of getting lice by wearing a yarmulke from the communal basket. Yes, lice generally are more common among kids than adults—but the yarmulkes that wind up in the “take one if you need one” basket often are leftovers from a recent bar mitzvah or bat mitzvah (a coming-of-age ritual traditionally done at age 13)—so they were worn mostly by preteens and teenagers.

Lice avoidance: Remember to bring your own yarmulke! If you are the forgetful type, keep a few spares in places like the glove compartment of your car, your briefcase, coat pockets, etc. (One of my colleagues keeps a yarmulke in his wife’s purse—with her permission, of course.)

Burning candles and incense. According to a study from Maastricht University in the Netherlands, after candles and/or incense were burned in the usual manner in chapels and churches of various sizes, the concentration of toxic polycyclic aromatic hydrocarbons (PAHs) in the air increased by a factor of four to 10. PAHs and other types of particulate matter that form when certain substances are burned have been linked to increased risk for lung cancer and other pulmonary diseases. The irritants in smoke from candles and incense also can also trigger asthma attacks in susceptible people, Dr. Schaffner added.

Smoke screen: If your place of worship is not well-ventilated and you have any sort of pulmonary condition or extra sensitivity to airborne irritants, sit as far away from the candles or incense source as possible, preferably near an open window or door. If a lit candle or incense thurible is carried around the church, hold a clean handkerchief over your mouth and nose as it passes your pew.

Molds. This hazard isn’t limited to houses of worship, of course. But many churches, synagogues and mosques are located in old buildings, and old buildings frequently are contaminated by mold…and even newer buildings aren’t immune. Plumbing leaks, poor insulation, large carpets that are shampooed frequently—all of these factors may turn churches and synagogues into “petri dishes” for mold. Some molds can trigger allergic reactions or asthma attacks in sensitive people…others are known to produce potent toxins and/or irritants, Dr. Schaffner noted.

Best: If you find that you often have respiratory symptoms after visiting your house of worship, talk to the trustees about having the premises inspected by mold-remediation experts—so that you and your fellow worshippers can breathe easier.

Bottom line: There’s no need to let concerns about getting sick from your church or temple deter you from your religious observances, Dr. Schaffner said. Your risk is very low if you follow the common-sense precautions above.