The launch was also delayed by a computer problem and Nasa had held the countdown at the 20-minute mark.
Persistent rain and heavy clouds glowered over the Kennedy Space Centre and the launch was scrubbed 90 minutes into a two hour window of opportunity, which has begun at 1747 GMT.
Poor weather causes Nasa a number of concerns. The thick clouds raise the possibility of a lightning strike. They also mean that the heat-resistant tiles on the shuttle could get wet, which would damage them. Finally, the low cloud means that visibility is too poor for landing if the shuttle had to return to the Kennedy Space Centre immediately after launch.
Second chance
The next possible launch is at 1744 GMT on Tuesday. The weather forecast is better for this time, but still not good. However, if this opportunity is missed, then the launch will be postponed until 9 February.
The launch was also delayed by a computer problem and Nasa had held the countdown at the 20-minute mark.
The computer in question sends the signals which cause the separation of the two rocket boosters and the external fuel tank after launch. The problem, which caused a week's delay to another shuttle in 1995, was quickly solved.
The purpose of the 11-day mission is to produce the most complete three-dimensional map of the Earth's surface ever made.
The Shuttle Radar Topography Mission (SRTM) will produce the data with a 60m (196ft) radar mast - the longest rigid structure ever deployed in space.
Engines safe
Nasa has said it is satisfied that the space shuttle Endeavour's engines are safe for launch.
Officials at Cape Canaveral in Florida had considered postponing the launch after revealing that the space shuttle Discovery had flown six times with a faulty engine component that should have been scrapped.
But shuttle programme manager Ron Dittemore said on Sunday: "We have reviewed the data and concluded that the engine is safe to fly."
Faulty part
A faulty turbine seal, which should have been discarded, was instead installed on the shuttle Discovery but Mr Dittemore said there was very little chance that a similar mistake had been made on Endeavour.
The damaged component measures 8.9cm by 1.3cm (3.5 inches by 0.5 inches) and is part of a seal that forces hot gases in the shuttle's three main engines through turbine blades.
Engineers only discovered the fault on Discovery because of some unusual signs of wear and tear during a routine servicing.
Had the joint given out during launch, the Discovery team may have faced an emergency landing.