What city does Scrubs take place in?

The filming of Scrubs takes place in Los Angeles, California in the North Hollywood Medical Center (a non-operational hospital).

The fictional place that Sacred Heart is located in Scrubs is known as "San DiFrangeles". Which happens to be a mixture of the name "San Diego, San Francisco, and Los Angeles. However in the episode "My First Kill" in Season 4, Molly (played by Heather Graham) implies that they are 3 hours behind "Greenland time" which would place them either on the East Coast or Midwest (depending on which "Greenland time" they were referring to)

In the episode My Best Friends' Baby and My Baby's Baby in season 6 Dr. Cox is reading a newspaper titled the Los Angeles Times, and then starts to eat the newspaper because Jordan is driving him crazy.

In one episode Turk gives out his phone number as (916) CALL-TUR (225-5887) 916 is a Sacramento (and small surrounding cities) area code. It may point to the hospital being in that area, but as a cell phone it could just mean that Turk is from that area.

However, in the episode where Dr. Cox had to do shifts on the ambulance the EMT patch on the jacket is a NJ Dept. of Health patch. J.D. also refers to Sandwiches as hoagies which is definitely East coast, especially Philly and South Jersey. There are also instances where the cars have Jersey plates on them but also California plates. However, they do drive to Vegas, which obviously would take a really long time from the east coast

They also road trip to Seattle when JD wants to go see Kim's first ultrasound, and the road trip takes less than a day, which implies that the hospital is likely somewhere in Northern California.