The hallmark symptoms of borderline personality disorder are maladaptive behavior and impulsive emotional reactions. However, the condition is occasionally associated with cognitive alterations. Recently, it has been found that the function of the basal ganglia and the hippocampi might also be affected. Hence, deterioration in learning and memory processes associated with these structures is expected. Thus, we sought to investigate visually guided associative learning, a type of conditioning associated with the basal ganglia and the hippocampi, in patients suffering from borderline personality disorder. In this study, the modified Rutgers Acquired Equivalence Test was used to assess associative learning in 23 patients and age-, sex-, and educational level-matched controls. The acquisition phase of the test, which is associated primarily with the frontostriatal loops, was altered in patients with borderline personality disorder: the patients exhibited poor performance in terms of building associations. However, the retrieval and generalization functions, which are primarily associated with the hippocampi and the medial temporal lobes, were not affected. These results corroborate that the basal ganglia are affected in borderline personality disorder. However, maintained retrieval and generalization do not support the assumption that the hippocampi are affected too.