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I've used bottles few times to bottle home beer. Recently I've found that inside them there are small spots that remain there even if I rinse them with water.

Should I worry about them? It's safe to put new beer into such bottles?

If it's not safe what is good option to clean those?

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An overnight soak in PBW or oxyclean always works well for freeing up beerstone and other deposits for me. The soak should start with the warmest tap water you can get. PBW is more expensive but I think it works better and the two are not equal when it comes to the tough stuff to get off, IMO.)

If there is still stuff stuck to the bottles and I am really hard up for bottles I'll have the bottle brush at the ready while the bottles are still wet after the soak. At that point if stuff still doesn't come out toss the bottle. Its not a guarantee to be unsafe, but bad beer, or overcarbed beer or exploding bottles isn't worth the cost of a few new bottles.

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I use bleach-and-water for sanitizing. I always have a bucket of about 30 litres of bleach-and-water sitting on my brewing counter.

After a month or two, I make myself a new bucket of sanitizer. Instead of dumping out the old sanitizer, I transfer it to another bucket and use it for bottle cleaning. Most bottles don't need any cleaning (just a rinse), but for the ones that do, I just fill them with this old sanitizer and leave them for a week or two. They usually end up perfectly clean after this.

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    Bleach solutions are not all that stable after 24 hours. The disinfecting power fades rapidly of a 10% solution. You obviously see no ill effects though. – brewchez Sep 6 '16 at 11:42
  • Man, I am jealous. With the kids and no closed area around, I don't have that luxury. – Robert Sep 6 '16 at 20:12
  • @brewchez: I wonder if that is one of the many homebrewing myths. As you said, I'm not seeing ill effects of this. I'd say that over 95% of my sanitizing happens with bleach solution that is over 24 hours old. On average, it's probably 3 weeks old. – Jeff Roe Sep 6 '16 at 20:21
  • The 'dangers' of using bleach as a sanitizer may be a myth. I am not commenting per se towards that. The rapid decrease in the oxidation potential of 10% bleach in water is not however mythology, its chemical reality/fact. Again, you see no ill effects however. – brewchez Sep 7 '16 at 10:27
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Cleaning involves removing the stuff you can see. As others have mentioned, a good bottle brush is the most common tool. I've also had success using a water pick (dental hygiene tool) to remove stubborn spots the bottle brush didn't get.

Next you need to Sanitize which kills most organisms. It is not usually necessary to Sterilize which removes all organisms. Star San is the most common sanitizer. Be sure to follow the directions at this step as carelessness can result in a lost batch. There are numerous resources on Google and YouTube if you're new to the hobby.

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Generally I'd always rinse bottles after they are finished, or at least at the end of the night.

You can try a bottle brush.

Depending on the kind of bottle, you can put it in the dishwasher. Works for e.g, Grolsch swingtop bottles.

If that doesn't get the spots out, then the beer probably will not get them out either.

  • I know that with my very first batch, oh so many years ago, I put my bottles through the dishwasher and no one died from drinking what was a fairly decent beer even for my young palate. I've since learned that detergent leaves residue on the bottles which can contribute to problems in the final product so a good soak in a sanitizing solution is the best bet (after a good cleaning beforehand). – linhartr22 Sep 6 '16 at 19:44

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