It could be so many things! Is it a mildew type smell, a damp smell, urine smell, what are we talking about here :)? If you think it's coming from the toilet, try drop in tablets for the tank and double check that the tank doesn't have a smelly buildup inside. Check the shower curtain for mildew as well.
The flavor of the smell, if you'll pardon the expression, is your best clue to the source. If it's a musty, mildewy smell, it's probably mold. This could be on a wall or ceiling surface (even hidden behind wallcoverings), it could be moisture getting inside the wall, or possibly a drip under a sink. Also could be a bad seal under the toilet, leaking water onto the subfloor or framing below.
If it's a sewer-gas smell, it's possible that one of your fixture drains was plumbed without a
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P-trap--the U-shaped section of a drain pipe. This remains partially filled with water to prevent sewer gas from rising up into your house.
You also might want to check your sink drains. Crud can build up on the inside enough to smell, especially with all the soap used in the bathroom.
Try sniffing you drain. We had a rancid smell in the bathroom once. Turned out that the slow draining sink was the culprit. Cleaned it up using a hand snake (Lowe's for less than $5) and a rinse with hot water and Borax. Now I just pour 1/4 cup of Borax and rinse with hot water once a month or when I remember to do so. No more smell.
If it's a sewer-gas smell, it's possible that one of your fixture drains was plumbed without a ...»
You also might want to check your sink drains. Crud can build up on the inside enough to smell, especially with all the soap used in the bathroom.