A high resolution Navy Coastal Ocean Model (NCOM) simulation of the Gulf of Mexico sea surface height (SSH) is compared to JASON altimeter observations for the period 2002 to 2006. The NCOM model uses the combined sigma and z-level coordinate in the vertical that allows for terrain-following sigma coordinates in the upper ocean providing for better representation in the shelf regions. In comparing the high resolution (1/24°, ~6 km) model outputs, a 5-day average simulated SSH anomaly is examined during the study period over the 16 altimeter repeat ground-tracks (ascending and descending) that transect over the Gulf of Mexico. Overall the SSH anomalies from model and altimeter were observed to be well correlated, however differences were observed in the shallower shelf and the warmer loop current waters. Implications of these results in model derived upper ocean heat budgets of the region will be addressed.