I've seen several threads on BP where whether or not caulking in the base of a toilet is a good idea has been discussed. Seems the general concensus is to NOT caulk them. I vehemently disagree!

The main reason given for not caulking them in is so that in the event a wax ring fails, the swill can run out into the floor and be seen so one knows theres a problem. The major concern is that te subfloor doesnt rot.

Over the years, I have renovated many dozens of bathrooms and I would say about 90% of them had rot issues due to leaks at the flange. My question is, do the wax rings fail us or do we fail the wax rings? IMO, it's the latter.

Setting a toilet is truly a shot in the dark. Its just not possible to check to ensure we've acheived 100% positive contact between flange-wax ring and wax ring-toilet. Being that damage from bad seals is so prevelant, It has never made sense to me that even the DIY gurus continue to teach the same old method.

Here's my reasoning in favor of caulking in the toilet base...

Toilets are attached to the flange with two wimpy little bolts. If you use only what comes in most flange bolt packages, the bolt is connected to the flange with nothing more than a plastic retainer washer. Then, the bolt passes thru an oversized hole in the toilet base, and the nut cannot be overtightened due to the potential the porcelain base can crack. Caulking in the base of the toilet is the added reinforcement needed to secure it in place so that it cannot move. Without caulk, how long do you suppose it would take the toilet to move with kids or large adults plopping down onto the seat? The smallest rocking or twisting could result in compromise of the seal.

Now, on to my reasoning for why a leak causing a rotted subfloor is no excuse not to caulk toilet...

It has never made sense to me that we take a shot in the dark and then neglect to take a step that can prevent the leak in the first place. So why does a leak have to cause damage? It doesnt!! I look at a bathroom as a wet environment where things like overspray from shower, overflowing clogged toilets, and overflowing bathtubs are a real concern and steps need to be taken to contain spills and at least reduce potential for damage.

When water runs thru a gap in the wax ring, where does it go? It flows down over the outer edge of the flange. On 100% of the floors with rot, there is a gap between the flange and the flooring. On vinyl floors, often the edges of vinyl have curled because the installer wasnt worried about full contact with glue or a precision cut, as the toilet will cover it. With tile floors, the cuts are often jagged, with good sized gaps because again, it will be covered. In both instances a small trickle at each flushing, which is likely the case with most failures, will never flow out where it can be seen. The water will take the path of least resistence, and take up residence in the exposed underlayment and subfloor.

Here's how I prep for setting a toilet...

1. If flange is metal and is rusty or a painted steel with paint peeling, replace it.
2. If old toilet is being reinstalled, clean outlet area well, remive existing caulk if present, and clean perimeter of toilet base with thinner.
3. If keeping existing vinyl flooring, cut away any curled edges. If vinyl is loose, staple edges down securley.
4. Always buy an extra plain wax ring. Cut a piece from it and "butter" entire area of toilet outlet that will come in contact with wax ring. Use finger to spread evenly and body heat and friction will ensure wax is bonded to porcelain. (Note: How many times have you pulled a toilet and the wax ring pulled away cleanly frome toilet outlet? Buttering makes sense!)
5. Now, cut chunk of wax and fill the void between flange and flooring. Again, use finger to smooth it out uniformly so you know all gaps are filled and wax is smoothed out onto surface of flooring.
6. Using same method, butter entire surface of flange being sure to fill all unused holes and screw heads.
7. Now, install bolts onto flange. Have extra nuts in hand and instead of using plastic retainers, securely attach bilts to flange with nut. Measure distance from each bolt to wall and ensure they are both horizontal to wall an centered on flange.
8. Fill bolts slots with wax and smooth over.
9. Take new wax ring out if package and run finger around flat bottom surface of wax repeatedly to warm it up. Now set it onto waxed surface of flange centering it over hole. Twist it as you push down into place. Now use some of the extra wax ring to "caulk" where wax ring meets flange. This is so that as ring compresses and is pushed outward it slides into soft wax.
10. Ready to set toilet. Straddle toilet and lift over flange, keepin bottom of toilet parallel with floor and lower straight down over bolts and onto wax ring. Hold toilet as level as possible and twist it slightly from side to side as you push down. Its good to have someone help guide it and to help ensure that toilet is straight when it hits its final resting place. The idea is to move it as little as possible once wax ring is fully compressed.
11. Now install nut. Go back and forth from on side to the other a you tighten, till both are snug. Overtightening will first bend flange and then crack porcelain.
12. CAULK THAT SUCKER IN!! If you want to leave and inch in the back uncaulked so a leak will show, thats fine.

I also seal entire perimeter of bathroom floors. I tile most, and usually use porcelain tile with a body color that matches surface so that I can cut tile base. I caulk in the base with siliconized acrylic caulk in a matching color. With wood base, I apply a small bead of siliconized acrylic toward back edge of bottom of base before setting it into place. Depending on flooring, I sometimes then caulk base to floor. I dont do this unless I have caulk that matches well with flooring. Vinyl cove base? I hate it. But when its used I caulk it after adhesive has set up.

Everything in remodeling is about the details. Thinking thru every aspect of a job and taking even the smallest preventative steps can save headaches and money down the road.

Another small step that can prevent damage is sealing perimeter of dishwasher hole I caulk cabinets and back wall to floor and if there is a gap between cabinets and wall, I create a dam there. If DW leaks water has nowhere to go but out onto floor. Same with those pesky sink drain leaks. Seal perimeter of cabinet and fill plumbing holes with Great Stuff foam if necessary. Simply sealing edges so that water cant soak into edge grain of cabinet bottom will prevent the major damage we see. If its a solid wood or veneered bottom, an extra coat of sealer before silicone is a good idea.

As with all my "opinions"... Take what you can use and leave the rest!