An alternative to clinical trial paper-based data collection (PDC) is internet based electronic data collection (EDC), where the investigators over the internet enter data directly in the electronic database by themselves. In our study we considered clinical trial as a business process. Our objective was to model PDC and EDC process and to estimate the difference of the costs of PDC and EDC process for a sample clinical trial based on these models. We used Extended Event-driven Process Chains (eEPC) modeling technique to model PDC and EDC process. In order to evaluate the costs of the processes we assigned costs functions to each process function which appears in the model. The parameters which appear in these functions include efforts, staff prices and data quality parameters. We estimated the values of all these parameters and performed costs calculations for a sample clinical trial. Through an analysis and modeling efforts we identified sub-processes which contain main differences affecting duration and costs of the PDC and EDC process: data gathering at the research center; monitoring; and data management. The most significant model difference between PDC and EDC process appeared in data management sub-process. For the sample clinical trial considered in our simulation study and our parameters estimations the EDC process decreased data collection costs for 55%. For different scenarios of parameters variations we show that the EDC process may bring from 49% to 62% of savings when compared to PDC process.