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ABSTRACT One of the biggest challenges in estimating the elastic, transport and storage properties of shales has been a lack of understanding of their complete pore structure. The shale matrix is predominantly composed of micropores (pores less than 2 nm diameter) and mesopores (pores with 2–50 nm diameter). These small pores in the shale matrix are mainly associated with clay minerals and organic matter and comprehending the controls of these clays and organic matter on the pore‐size distribution is critical to understand the shale pore network. Historically, mercury intrusion techniques are used for pore‐size analysis of conventional reservoirs. However, for unconventional shale reservoirs, very high pressures (> 414 MPa (60 000 psi)) would be required for mercury to access the full pore structure, which has potential pitfalls. Current instrumental limitations do not allow reliable measurement of significant portions of the total pore volume in shales. Nitrogen gas‐adsorption techniques can be used to characterize materials dominated by micro‐ and mesopores (2–50 nm). A limitation of this technique is that it fails to measure large pores (diameter >200 nm). We use a nitrogen gas‐adsorption technique to study the micro‐ and mesopores in shales and clays and compare the results from conventional mercury porosimetry techniques. Our results on pure clay minerals and natural shales show that (i) they have a multiscale pore structure at different dimensions (ii) fine mesopores, with a characteristic 3 nm pore size obtained with N 2 gas‐adsorption are associated with an illite‐smectite group of clays but not with kaolinite; (iii) compaction results in a decrease of pore volume and a reduction of pore size in the ‘inter‐aggregate’ macropores of the illite‐smectite clays while the fine ‘intra‐tachoid’ mesopores are shielded from compaction; (iv) for natural shales, mineralogy controls the pore‐size distributions for shales and the presence of micropores and fine mesopores in natural shales can be correlated with the dominance of the illite‐smectite type of clays in the rock. Our assessment of incompressible 3 nm sized pores associated with illite‐smectite clays provides an important building block for their mineral modulus.