The short-term variability of the methane column has been analyzed based on ground-based observations and numerical modeling at the St. Petersburg NDACC station for 2009-2016. The methane variability for different atmospheric altitude layers is presented. Short-term methane variability is found to be significant compared to long-term trends. The results of numerical experiments with the global chemistry-transport model of the troposphere and stratosphere demonstrate that short-term methane variability is basically defined by methane concentration changes between an altitude of 5 km and 20 km.