Transmission electron microscopy-energy dispersive X-ray analysis (TEM-EDX) represents an effective tool for determining the stoichiometric composition of clay minerals, but the methodology is often hampered by analytical difficulties. Studies of beam-sensitive minerals, such as smectites, are associated with low count intensities and dynamic loss of cations (e.g. K+, Na+, and Al3+), which can lead to erroneous quantifications of composition. After exploring how to minimize cation migration by reducing the beam current density to <5 pA cm–2, the most reliable and consistent compositions were determined using 1 μm2 area measurements of particles acquired in normal TEM mode where the electron beam was parallel, the degree of specimen damage was at its minimum and good acquisition intensities (>10,000 cps) were acquired. Based on 528 TEM-EDX area analyses, the composition of Wyoming montmorillonites (SWy-1, SWy-2, and SWy-3) was studied in their natural and Ca-saturated states from thin (<50 nm thick) particle aggregates lying on lacey carbon films. Overall, the TEM-EDX results confirmed the heterogeneous charge distributions of montmorillonite at the particle and sample levels. The average composition per formula unit of SWy-1 to -3 was determined as: (Na0.12Ca0.04Mg0.03K0.02)(Si3.91Al0.09)(Al1.57Mg0.27Fe0.19)2.03 O10(OH)2 · nH2O, where the tetrahedral and octahedral layer charges are –0.09 and –0.19 per O10(OH)2, respectively, and the total layer charge ranges from –0.25 to –0.30 per O10(OH)2 (mean of –0.28). This study demonstrates how TEM-EDX can provide new insight into the natural heterogeneities of smectite chemistry as long as adequate calibration and specimen damage control procedures are implemented.