Nano-ball allophane is a hydrous Al silicate with a hollow-sphere morphology that contains some defects or pores along the spherule walls. Enlargement of the pore openings by dilute alkali treatment was confirmed by cation exchange capacity determinations using various alkylammonium cations as replacement cations. An allophane sample with a low Si/Al ratio (0.67) was equilibrated with 10 mM CaCl2 (pH = 6.0) and the Ca2+ retained was extracted using aqueous 1 M NH4Cl or alkylammonium chloride salts. The Ca2+ extracted by NH+4 was 15.1 cmolc kg−1, but CH3NH+3 (mean diameter = 0.38 nm) only extracted 7.9 cmolc kg−1 of Ca2+. After 10 mM NaOH treatment (0.25 g:100 mL) of the allophane, the Ca2+ extracted by NH+4 was 29.7 cmolc kg−1, 29.6 cmolc kg−1 by CH3NH+3, and 29.4 cmolc kg−1 by (CH3)2NH+2. The extraction of Ca2+ by the large C2H5NH+3 cation (mean diameter = 0.46 nm) only decreased to 26.1 cmolc kg−1, indicating that pore diameters were enlarged from ~0.35 to 0.45 nm. The significant increase in Ca2+ retention after NaOH treatment was attributed to the dissociation of increased numbers of newly exposed silanol groups in the enlarged pores. The low Si/Al ratio of the NaOH-dissolved material (0.35) and the decreased intensity of the 348 cm−1 IR band also suggested selective dissolution of the pore region. For allophane with a high Si/Al ratio (0.99) and much accessory polymeric Si, dissolution of polymeric Si and of the pore region occurred simultaneously. Alkali treatment produced a smaller increase in pore size and Ca2+ retention for allophanes with large Si/Al ratios than for allophanes with small Si/Al ratios. It was concluded that by altering the dilute alkali treatment conditions and varying the Si/Al ratio of allophane, the extent of structural modification or pore enlargement of the hollow spheres might be controlled.