Apple has posted instructions for developers to ensure that they download valid copies of Xcode. This follows the discovery of XcodeGhost, a counterfeit version of Xcode infected with malware, which was then used to compile apps that were also infected.
First, Apple encourages developers to only download Xcode from the Mac App Store, or from the Apple Developer website, leaving the Mac's Gatekeeper on to protect against tampered software. From Apple:
When you download Xcode from the Mac App Store, OS X automatically checks the code signature for Xcode and validates that it is code signed by Apple. When you download Xcode from the Apple Developer website, the code signature is also automatically checked and validated by default as long as you have not disabled Gatekeeper.
Apple also posted instructions for validating your copy of Xcode, which you can find below.
To verify the identity of your copy of Xcode run the following command in Terminal on a system with Gatekeeper enabled: spctl --assess --verbose /Applications/Xcode.app
where /Applications/ is the directory where Xcode is installed. This tool performs the same checks that Gatekeeper uses to validate the code signatures of applications. The tool can take up to several minutes to complete the assessment for Xcode.
The tool should return the following result for a version of Xcode downloaded from the Mac App Store: /Applications/Xcode.app: accepted source=Mac App Store
and for a version downloaded from the Apple Developer web site, the result should read either /Applications/Xcode.app: accepted source=Apple
/Applications/Xcode.app: accepted source=Apple System
Any result other than 'accepted' or any source other than 'Mac App Store', 'Apple System' or 'Apple' indicates that the application signature is not valid for Xcode. You should download a clean copy of Xcode and recompile your apps before submitting them for review.∂