Companies or organizations can develop custom apps for iPads or iPhones, to do that, they need to use provisioning profiles to install the apps. The provisioning profile contains the information required to make the iPads or iPhones install the app.
To get the provisioning profile for the company, three things are needed: a valid Enterprise Developer Account, a provisioning profile, and an app distribution bundle. the custom company app can be distributed only for the employees from the company's network without going through the apple app store.

source: McGraw Hill - iPad and iPhone Administrator Guide