Well, yes, all my contacts came from my Windows PC using MS Outlook. Unfortunately, that PC was recently stolen, so I was glad to still have my contacts in my iPhone. Then they disappeared.
I did notice today that although nothing is left in my Contacts, when I start a new text message and start typing letters in the To: address there appears a list of some people who were in my Contacts. I just don't know how to find these people otherwise.
I wrote in another discussion about contacts - I also had the same problem, all my contacts dissappeared after iOS 6.1 (iPhone 4) in the iPhone contacts, however, all contacts are visible in Macbook and in iCloud.
Try to create a "dummy" new contact in your iPhone (using your phone, not through iCloud or Macbook) and add it to contacts. It solved my problem and now all contacts are visible. Seems like some display problem in Contacts app.
For me, this is what worked:
I noticed the last contact I added was in the Address Book, but all others were gone or missing.
I went to MS Outlook and ran the Sync program. Unchecked all options. Restarted the computer. Made sure the iCloud stuff was turned off on the phone and restarted it too for good measure.
When the macbook came back up when into outlook then MS Sync and turned contacts back on. Then connected the iphone and told it to replace all contacts. It worked.
Good luck. There is no one solution that seems to work for everyone, but testing different settings will hopefully get you to the point where your contacts go back onto the phone.