Can I pray with a stain on my clothes?

Yes, in most cases. Most stains, like coffee, food, ink, paint or grass, are not impure, so you can pray in those clothes. Only stains from impure substances (najis), such as urine, feces or a large amount of blood, need washing first. If you're not sure what a stain is, your clothes count as clean.
Dirty isn't the same as impure
Islam has a specific list of impure things. Ordinary dirt and messy stains aren't on it. Being tidy is good manners, but it's not what makes a prayer valid.
- Not impure: food, coffee, tea, ketchup, ink, paint, makeup, grass, mud, sweat and saliva.
- Impure (najis): urine, feces, vomit (in most schools), pre-ejaculate (madhy), and blood. Most scholars excuse a small amount of blood, like a dot from a shaving cut.
- Differences: semen and alcohol are debated among the schools. Ask about the view you follow.
Paint and ink are fine as long as nothing on your skin blocks water during wudu. Clothes just need to be clean and decent. See Can I pray in jeans?
Certainty beats doubt
The basic rule is that things are pure until you know otherwise. When a man thought he might have passed wind in prayer, the Prophet ﷺ said he shouldn't leave "unless he hears sound or smells something" (Sahih al-Bukhari 137). Scholars apply the same principle to clothes: a mystery mark on your sleeve doesn't make it impure. Only certain knowledge does.
If you keep inspecting your clothes before every prayer, that's a sign of overthinking, not piety. See What is waswas and how do I deal with it?
If you find out after praying
Once, while leading the prayer, the Prophet ﷺ took off his sandals. Afterward he explained that Jibril had told him "there was filth in them," and he continued the prayer without starting over (Sunan Abi Dawud 650, graded sahih). Based on this:
- Maliki and many Hanbali scholars: if you didn't know about the impurity, your prayer is valid. Malikis recommend repeating it if the prayer's time hasn't ended.
- Shafi'i and Hanafi: repeat the prayer, with Hanafis only counting impurity larger than a small coin's area.
If you discover it during the prayer and can remove it quickly, like taking off a jacket, do so and carry on. The same idea applies to shoes. See Can I pray with my shoes on?
- Food, ink, paint and dirt stains don't stop you from praying.
- Only impure stains like urine, feces or lots of blood need washing.
- If you're unsure, treat your clothes as clean.
- Schools differ on repeating a prayer when you find impurity later.
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