I came across permission issue, were only a single user gets "Access Denied" on SharePoint site. The user was able to access the site (his was added to the Visitors group) for one day, then all of a sudden he cannot access the site. I checked his permission and I could not see any reason for this user to get the error. I even tried to give him full control and that didn't work. I have created a new site collection and added him as a Visitor and he could access the newly created site collection. Since troubleshooting permission issues are difficult, I did download third party tool (i got the 14 days trial version) and installed it on a development machine, then moved the site to the development farm and the user still got the access denied error. I ran the tool and could not see any special permissions. So after further trials and errors, I came to the following resolution:
1. Added the user to the Site Collection Administrator (SCA) group, and now the user is able to access the site without issues.
2. Removed the user from the SCA group and that removed all his permissions, and he got the access denied error.
3. Added the user back to the Visitors group and now he could access without issues.
Not sure why the above steps fixed the issue, but I suspect by adding him to the SCA group and removing him, which remove the user's permissions from all SharePoint objects, and by adding the user again is like adding him for the first time. I guess at this point we will have to wait and see if the user runs into this issue again.