Although it is widely acknowledged that protocol design plays a crucial role in the success of clinical research studies, how protocols have changed over time and the impact of these changes on clinical trial performance have never been quantified. To measure protocol design trends, the Tufts Center for the Study of Drug Development analyzed data on 10,038 unique phase 1-4 protocols conducted between 1999 and 2005. Tufts Center for the Study of Drug Development analyzed study conduct performance data on 57 individual phase 2 and 3 protocols administered at US-based investigative sites. The results of this study indicate that the number of unique procedures and the frequency of procedures per protocol have increased at the annual rate of 6.5% and 8.7%, respectively, during the time period measured. Investigative site work burden to administer each protocol increased at an even faster rate of 10.5% between 1999 and 2005. Additionally, during this time period, study conduct performance--that is, cycle time and patient recruitment and retention rates--worsened; and the number of protocol amendments, observed serious adverse events, and length of case report forms increased substantially. Implications of these results for simplifying protocol designs and minimizing negative effects on study conduct performance are discussed.