I won't post the whole long article but if you want to read about this
http://community.discovery.com/eve/forums/a/tpc/f/9401967776/m/9241965418
Using a variety of popular make full-size trucks and a 75-mph wind speed, the vehicles were tested in a wind tunnel with the tailgate up, down and removed.
One had a mesh gate made of duct tape. One had an adjustable tonneau cover that could cover various portions of the truck bed.
The wind tunnel balance-measured all six components of aerodynamic force and moment. Drag coefficients (Cd) for the trucks were normalized so the focus could be kept on box aerodynamics. All the measurements showed the same basic results-a small increase in drag with the tailgate down and a larger increase with the tailgate off. These measurements were made with the vehicle directly aligned with the stream of air.
Another interesting result was that lowering or removing the tailgate caused a larger increase in drag on 61/2-ft. boxes than on 8-ft. boxes. Installing the mesh gate was shown to yield the worst results of all. In one example, the Cd increased from .48 to .53 with the mesh gate in place of the solid tailgate.
What does work is a tonneau cover. Interestingly, a partial 20-in. cover placed nearest to the tailgate did 88% as well as a full tonneau cover. On an 8-ft. box, the estimate is that the improvement in fuel economy with a full tonneau could be 1.35 mpg, or a saving of 243 gallons over 100,000 miles of driving. Conversely, the same vehicle without the cover and with a mesh tailgate got 1.28 mpg worse mileage than a vehicle with the tailgate up and no cover.
The wind tunnel and road tests answer the question of whether removing the tailgate is a good idea. What it doesn't answer is why. For this, Cooper and his group used CFD software to model the flow of air in and around the box of a pickup truck. They found that with the tailgate up, a bubble of air forms in the truck bed that allows air flowing from the front to the rear of truck to ride up and over the vehicle. When the tailgate is removed, there's a stronger downwash that forces some of the air to flow over the rear bumper. This stronger downwash behind the cab is what's responsible for the increased aerodynamic drag.
Among the conclusions in his paper, Cooper points out that for an average pickup, the fuel saved by leaving the tailgate up is likely to be on the order of 122 gallons over 100,000 miles of freeway driving. On an individual basis, this is not a lot of fuel or a lot of money. However, when you apply this to the millions of vehicles out there, this really is large.
And from a safety standpoint, having the tailgate down makes it and not the bumper the first point of contact in a rear-end collision. Based upon the data-and the cost of gasoline-having a full or partial tonneau might be worth the investment.