Students often have an oversimplified view of biological facts, which may hinder subsequent understanding when conceptual complexity gives rise to cognitive conflicts. To avoid this situation here, we present a PBL approach for the analysis of Ehlers-Danlos syndrome (EDS), which integrates a variety of topics in cell biology, genetics, and molecular biology, and it is used to illustrate the inherent complexities in some classical biological concepts. Students of two different courses analyze phenotypic, cellular, and molecular characteristics of EDS. Effect of mutations on collagen synthesis on collagen genes' expression and regulation or on connective tissues is reviewed and discussed. Information retrieval is used to develop students' skills in web-based molecular biology tools. Student interest and motivation is increased with the development of diagnostic protocols for a tissue biopsy and for an EDS causing mutation. Expected learning outcomes after completion of the project are also presented. (Contains 5 figures and 1 table.)