Purpose: It is thought that proteoglycan (PG) alterations, collagen matrix reorganisation and the onset of corneal transparency in the developing avian cornea might be related events. The current histochemical study was designed to establish the character and distribution of corneal PG filaments in relation to collagen organisation during tissue morphogenesis. Methods: Corneas from days 13–18 developing chicken embryos were treated with cuprolinic blue (CuB) to examine sulphated PGs by transmission electron microscopy and quantitative image analysis. Results: On developmental day 13, corneas contained poorly defined lamellae and a large number of both small and large CuB-stained PG filaments, randomly distributed and often in collagen-free regions. By day 14 and after, the large CuB-stained PG filaments were much less abundant. At this time, too, collagen fibrils displayed an axial alignment and an occasional periodic arrangement of small CuB-stained PG filaments along their axes. By developmental day 15, lamellae were well formed and continued to increase in number and size thereafter. Between developmental days 16 and 17, there was a significant increase (p < 0.001) in the number of small, collagen-associated PG filaments. This increase persisted into day 18. Conclusions: The size, number and distribution of sulphated, CuB-stained PG filaments in the developing avian cornea change over time. This is particularly true between developmental days 13 and 14 and between days 16 and 17, concurrent with previously documented structural changes.