This case study involved year 9 students carrying out project work in biology via problem-based learning. The purpose of the study was to (a) find out how students approach and work through ill-structured problems, (b) identify some issues and challenges related to the use of such problems, and (c) offer some practical suggestions on the implementation of problem-based project work. Data sources included observation and field notes, students' written documents, audiotapes and videotapes of students at work, and student interviews. The findings showed that several students initially experienced difficulties in identifying a problem themselves but after discussing with family and friends, were able to overcome this initial barrier and subsequently formulated personally meaningful problems for investigation. The ill-structured problems stimulated students to pose questions which charted their courses of action, leading to independent inquiry. Students were led to investigate multidisciplinary elements beyond the boundaries of typical school science, and also learned about different modes of inquiry. The issues and challenges identified included identifying a problem for investigation; asking questions to negotiate the learning pathway; deciding what areas to pursue, given a multitude of possibilities; and figuring out how to extract relevant information from the available mass. Implications of the findings for instructional practice are discussed.