A protection system for a gas analyzer is described which monitors gas pressure adjacent a sample cell included in the analyzer. The sample cell is connected via a gas/liquid separator to an input sample conduit. The measured pressure indicates when the separator is clogged with excessive liquid. A control circuit is provided which responds to selected pressure conditions by automatically controlling the valve to interrupt the flow of gas from the separator to the sample chamber. In this way, the sample chamber is protected against contamination by liquid. In the preferred embodiment, the sample chamber and the separator are automatically backflushed to remove any water contamination.