My bitch had her pups 12 days ago. This is her first litter and she is doing fantastic. My question is we have been sleeping next to her whelping box since she had them to make sure everything is ok with her and babies and wondered when will the right time be to leave her and babies threw the night without me staying with her.

It's up to you but we stayed with our bitches (one of us - usually my husband as I needed to sleep perhaps more than he did, so I could take over with the others during the daytime!) pretty much until mum wasn't in with them - which was for longer than 12 days.   Mine is a low to ground breed and it was all too easy for them to unintentionally lie on them, even with a pig rail round the box.    Perhaps setting up a baby-alarm might mean you'd hear if there's a problem?   Having a litter is a huge responsibility and a ton of work - and people wonder why puppies cost so much!!

For us it is usually around the three week mark.

A pup can get squashed even with you asleep at the side of the whelping box, as I found to my cost with one litter. I use a baby monitor to view and hear the pups once I start sleeping in my own bed again.

I once lost a puppy that was squashed at 4 weeks. Horrific so you do have to be very careful.