How does one interpret negative geopotential height values? I am using NCEP Reanalysis Geopotential height data and this is at 1000 mb and downloading it from here - 1000 Mb Geopotential height values and some of these values are negative for a particular date - May 12th 2014 00Z. I am aware of geopotential height anomalies - Geopotential height anomalies  and that these can be negative i.e. the average of a height surface is lower than than what it should be. But the negative values I am referring to are "raw" geopotential height values and not anomalies. 

When I sent them a note and asked them what that meant this is the explanation I got - "1000mb geopotential height could be negative if the contour line drawn around the surface of the earth connecting all 1000mb pressure intersected with the earth's surface. At the point where the height was negative, the 1000mb height is actually below the ground and pressure is low."

Can someone explain what that means as doing a google on  negative geopotential does not reveal anything meaningful ?
This likely means that the surface MSLP is less than 1000 mb.

If you are looking at a 1000 mb geopotential height, and the MSLP at a point is 995 mb, then the height of the 1000 mb geopotential surface would be below the ground, i.e. negative height.

Effectively the question was what does a negative difference of distance from a pressure surface mean? The answer is that the surface must lie below the frame of reference. In the example, the frame of reference is the ground and the surface is the 1000 mb surface.