Deficiencies in rational thinking skills are the source of many difficulties in science education. Characterization of these deficiencies is a first step in finding a possible remedy. The present paper describes an instrument for diagnosing students’ difficulties in causal reasoning while studying biology. The results provide evidence that, while studying various biological topics, students have difficulties in understanding logical relationships. Similar results were obtained from logically equivalent items in four different biological contexts. The two main difficulties found are (a) inability to organize events according to their correct temporal sequence and (b) inability to identify an event which had been caused by another (given) event. Possible implications for biology education are discussed.