The guarantee usually is for 2 years, but doesn’t apply in the following cases:
- Damage caused by using your Fairphone with other products that do not comply with the requirements and/or specifications for using with a Fairphone
- Damage caused by breaking or circumventing access limitation protection, beyond the standard root access of your phone, or by the improper usage of the root access
- Damage caused by installing third-party software
See: https://fairphone.zendesk.com/hc/en-us/articles/201166786-Warranty-and-Returns-for-your-Fairphone
Which OS are you planning to install? Currently there are only Fairphone OS and AOSP 4.2.2 supported. (And there is an unofficial port of Cyanogen Mod).