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OK to start off I'm not the smartest guy when it comes to cars but I'm learning. So I've read that this year of civic should only have 2 sensors but mine has 3 most likely because my civic has an after market exhaust system. The one on the manifold, after the manifold and on the cat. The one after the manifold is bad and I want to buy a new one to replace it but I am not sure which to buy.

 
Rep Power: 173

Well for starters what year and trim level do you have?

 
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If you can answer Poopies and post a picture of the sensor, we can point you in the right direction.

 
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my bad it's a 99 ex.

 
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I'm at work right now but I'll get that picture as soon as possible

 
Rep Power: 173

You're looking at part 41 here:
http://estore.honda.com/honda/parts/...=B++02&dl=#041

I assumed you had a 4 door automatic so you can change that in the top menu if you'd like. It should all be the same though. Now you might notice that the part goes for over $300.00. I'd recommend searching the part number on the Google and using another source. Just my $.02

BTW the Honda estore is not showing a sensor on the manifold. Now I'm intrigued!

 
Rep Power: 367

Mechanical problem related, not a bolt-on performance item, so moving to correct section.

 
Rep Power: 173

Oh snap! I missed that!

 
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A stock EX and SI models have a cat-back design: cat convertor is located farther down the exhaust as compared to other base models where the CC is welded to the manifold. Do you know if you a manifold or did a prior owner install after-market headers? In the pic below it shows headers (chrome) on the left and the stock manifold on the right. Either setup you should only have one primary sensor (pre-cat) and one secondary sensor (post-cat). A stock wiring harness would only have connections for these two sensors.

The one that you said is bad is the primary (upstream) sensor should be this one:
How do you know it's not working? related CEL?