Aldehyde-free, transparent chitosan aerogel is reported. The aerogel was prepared by thermal decomposition of urea to induce gelation of a chitosan solution, followed by solvent exchange to ethanol, and supercritical drying. Low urea concentrations (≤ 25 g L−1) result in transparent and highly mesoporous aerogels, while higher urea concentrations (≥ 30 g L−1) produce opaque, more macroporous aerogels. The high surface areas of > 400 m2 g−1, large mesopore volumes up to 3.5 cm3 g−1, and optical transparency of the low-urea aerogels indicate a high structural homogeneity at the mesoscale, and the properties comparable to previously reported transparent chitosan aerogels prepared with formaldehyde crosslinking. The macroscopic size changes of the wet gels indicate that microstructure formation is controlled by the timing of chitosan coagulation, which depends among others on urea concentration. The aldehyde-free, microstructure-tunable process provides a new series of transparent biopolymer aerogels with "true aerogel" mesoporous structures.