Calculations of atmospheric transmission through the M (5 microns) atmospheric window, at a resolution of 10 to the 3rd power are presented for sites at the Observatorio del Teide, Tenerife and the NHO, La Plama in the Canary Islands. We use a standard midlatitude atmospheric model and absorption line strengths for the known molecular species calculated at a height of 2.38 kms. It is demonstrated how the normal procedure for calibration of extinction can give systematic errors in the assessment of infrared flux both for photometry, using broad band filters, and for spectrometry.