This paper considers the use of log data provided by learning management systems when studying whether students obey the problem-based learning (PBL) method. Log analysis turns out to be a valuable tool in measuring the use of the learning material of interest. It gives reliable figures concerning not only the number of use sessions but also the interlocking of various course activities. The longitudinal study based on log analysis makes use of a new software tool, SPY US. Our study concentrates on using log data analysis in improving the PBL method used in learning diagnostic skills with the help of Virtual Patients.