Jonathan Heiliger, Facebook’s vice president of Technical Operations, has been the Palo Alto-based web giant’s public face when it comes to all things infrastructure. And today (May 3rd), he announced that he would leave the company at the end of the summer. After four years running Facebook’s infrastructure, he is handing over his job to Jay Parikh, who joined Facebook from Ning two years ago. Parikh will report to Mike Schroepfer, Facebook’s vice president of engineering. Heiliger, who also over saw Facebook’s internal IT needs is going to hand over that aspect of his job to David Ebersman. For now Heiliger has no concrete plans on what he will be doing next, other than helping some startups think about scale and infrastructure as an adviser,

After spending four years at Facebook — Heiliger joined the company in 2007 just before its mad dash to the top began — he said in an interview that he needs a breather. During his stay, Facebook has grown 20 times in size and with growth came significant challenges. “We have gone through a few close calls to significant disasters,” he says. “There were times when we were out of capacity with no more servers available.”

Jonathan oversaw Facebook’s global infrastructure and internal technology systems. Heiliger who joined Facebook after spending time at LoudCloud, Danger and GlobalCenter looks back at his time with the social web giant with fondness. “It was my fourth startup and frankly I didn’t think I had another startup in me,” he says. “We eclipsed many goals and set new ones.”

Of those goals, Heiliger speaks of recent launch of Facebook’s bespoke data center with much fondness. Well spoken and very dapper, Heiliger has often used his understated style and position at Facebook to rebuke and goad established giants into action. A repeat speaker at our first Structure conference, Jonathan chastised the chip industry for building processors and never really understanding the needs of web-centric companies such as Facebook.

His comments set-off a furor that eventually led to web giants and chip companies such as Intel and AMD working closely. More recently, Heiliger help shepherd the Open Compute project, that saw Facebook open source not only it data center designs but also share its server designs. The Open Compute project will be Jonathan’s legacy, for it has the chance of disrupting the server ecosystem.

When I asked Jonathan what surprised him the most during his stay at Facebook, he said it was how quickly the site grew. Today the infrastructure team is bigger, but he said that the same philosophy of experimenting and constant improvements is what will keep the company’s technology debt very low.

Heileger is one of the early Facebook team members that includes Adam D’Angelo, Charlie Cheever, Dustin Moskovitz, Jeff Hammerbacher and Matt Cohler. His decision to leave Facebook is an end of an era.

PS: Jonathan will be at our Structure 2011 conference. Be sure to say hello to him at the conference.