Pros
Atlassian, like a lot of the other SF bay area startups, has a lot of great perks – fun atmosphere, great office, stocked drinks, and food. They also have a lot of dedicated and smart people working there that makes coming into work fun. Besides the ubiquity of JIRA, I first heard about the company from a TED Talk several years ago (Dan Pink on Motivation – look it up, it's good) and wanted to work there ever since.
Cons
In a way, I felt like I was the victim of a bait and switch, and it seems like this is because it's a big company acting like a small startup. I interviewed for one role, and was offered something else, which I had accepted thinking that it would be just as good and similar. What I had found was a team going through transition – people leaving and management being replaced, and a project starting to come apart at the seams. To be honest, I should have asked more about the role before accepting it. Atlassian is going through growing pains, just as much as any other successful company in the SF bay area. You can gather this by also looking at the Cons of other reviews (even positive ones) – lack of career development, seemingly disorganized management., etc.