Background Medical knowledge encompasses both conceptual (facts or “what” information) and procedural knowledge (“how” and “why” information). Conceptual knowledge is known to be an essential prerequisite for clinical problem solving. Primarily, medical students learn from textbooks and often struggle with the process of applying their conceptual knowledge to clinical problems. Recent studies address the question of how to foster the acquisition of procedural knowledge and its application in medical education. However, little is known about the factors which predict performance in procedural knowledge tasks. Which additional factors of the learner predict performance in procedural knowledge? Methods Domain specific conceptual knowledge (facts) in clinical nephrology was provided to 80 medical students (3rd to 5th year) using electronic flashcards in a laboratory setting. Learner characteristics were obtained by questionnaires. Procedural knowledge in clinical nephrology was assessed by key feature problems (KFP) and problem solving tasks (PST) reflecting strategic and conditional knowledge, respectively. Results Results in procedural knowledge tests (KFP and PST) correlated significantly with each other. In univariate analysis, performance in procedural knowledge (sum of KFP+PST) was significantly correlated with the results in (1) the conceptual knowledge test (CKT), (2) the intended future career as hospital based doctor, (3) the duration of clinical clerkships, and (4) the results in the written German National Medical Examination Part I on preclinical subjects (NME-I). After multiple regression analysis only clinical clerkship experience and NME-I performance remained independent influencing factors. Conclusions Performance in procedural knowledge tests seems independent from the degree of domain specific conceptual knowledge above a certain level. Procedural knowledge may be fostered by clinical experience. More attention should be paid to the interplay of individual clinical clerkship experiences and structured teaching of procedural knowledge and its assessment in medical education curricula.