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The default white is very tiring for the eye after some hours.

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Many people have their computer displays set too bright, which cause eye strain. That my be your problem. Try reducing the display's brightness. – m_goldberg Apr 19 '14 at 16:52
closely related: Invert Colors Stylesheet White on Black – Kuba Apr 30 '15 at 11:16

I created own dark theme for Mathematica. It looks like dark theme

All stylesheets needed for that you can found here [repo]= You need to copy .nb files from repo [repo]/SystemFiles/FrontEnd/StyleSheets/ to your local Mathematica StyleSheets folder. After that you can choose stylesheet named as Dimad.nb (You also may set it as default stylesheet). Also there is Plot's functions color palette for dark theme in [repo]/Kernel/init.m. You need to add it's content to your local .Mathematica/Kernel/init.m file. Hope it helps.

PS: All was done for Mathematica 9.0, I didn't test it for other versions.

PPS: It uses Ubuntu Mono as default font. It can be obtained here

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This is truly beautiful. Thanks, community bot! – LLlAMnYP Apr 30 '15 at 11:49

I don't know how about you but I missed the fact it is built in since V 10.

Go Format -> Stylesheet -> ReverseColor:

enter image description here

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Now how can I set this as the default... – Andrew MacFie Feb 8 at 17:10
This is probably a bug but with Mathematica 10.4 Student Edition (on Linux), the output box does not invert color properly. – theindigamer Jun 30 at 19:45

The quickest thing might be to modify the default stylesheet and save it as a new one. You can find a good description of how to do that on David Park's Mathematica page

If you want a ready-made stylesheet, I've found David Park's PresentationsStyle stylesheet especially easy on the eyes. It not only uses a light brownish background but changes other styles so as to harmonize. If you own Park's Presentations add-on, then you already have this stylesheet. If you don't, you can obtain it as part of his newly-available FreePresentations add-on (which allows you to read documents prepared with the full Presentations but not conveniently to author new ones):

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