Although it is well established that funding source influences the publication of clinical trials, relatively little is known about how funding influences trial design. We examined a public trial registry to determine how funding source shapes trial design among trials involving antihyperlipidemics. We used an automated process to identify and analyze 809 trials from a set of 72,564. Three networks representing industry-, collaboratively, and non-industry-funded trials were constructed. Each network comprised 18 drugs as nodes connected according to the number of comparisons made between them. The results indicated that industry-funded trials were more likely to compare across drugs and examine dyslipidemia as a condition, and less likely to register safety outcomes. The source of funding for clinical trials had a measurable effect on trial design, which helps quantify differences in research agendas. Improved monitoring of current clinical trials may be used to more closely align research agendas to clinical needs.