My husband set a new toilet let it fill with water flushed it and went to the basement to check for leaks. There were no leaks but when he came back up there was no water in the bowl. He flushed it again and stood and watched it it takes about 3 minutes for the water to drain from the bowl. The water in the tank stays there and does not drain out.
Does anyone know what would cause this. He called the 1800# and the person did not have an answer. He also spoke to several people but no one that he spoke to has had this happen.

What brand toilet? Are there any other fixtures running when this toilet spontaneously empties?

Tell you what I think... remove the toilet bowl and set it up on a pair of sawhorses or similar. Then add water to the bowl and see what happens... if it empties there is a hole in the bowl somewhere (in siphon jet is best guess cause you cannot see inside that). There are also toilet bowl plugs that the manufacturers use to plug holes in ceramic... they can fail, too. You would not see leak downstairs as it is leaking into the waste line.

Better yet... just return the bowl... It is defective. It does not happen often... but it does happen. I think this should do it... unless you dropped a rag in toilet and that is siphoning toilet bowl... or something else? Hey let me know what you find... ok..

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Once more Massplumber's "bang on" Read on, Sometimes in casting the bowl there is a small bubble in the china. Instead of junking the bowl the manufacture will put a porcelain patch over the hole and send it on through. On occasion the patch will fail allowing the water to seep out of the bowl. If that's the case you would have a full bowl after you flushed and the bowl filled but some time later you would notice a drop in the bowl level. If you're worried about where the water's going, in both cases it drains back down into the sewer and not under the bowl on the floor.
As Massplumber sez, You have a defective bowl, have it reploaced under warranty! Good luck, Tom

Per your instructions they are going to pull it out and take it back.