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Biomedical engineering is a rapidly expanding field and it has been largely responsible for the improvements in the treatments of our patients. Many of the medical devices that are being marketed today were developed at universities and medical centers and this research is often supported by biomedical industry. University-industry partnerships are encouraged by federal and state funding agencies. However such relationships also raises the questions related to the conflicts of interests, appropriate protection of patients in clinical trials, full disclosures and monitoring of adverse effects of the use of drugs and devices, and many other ethical issues. University-industry cooperation is essential for invention of new biomedical devices and their rapid introduction to the market place. At the same time we need enforceable guidelines to avoid the pitfalls which may undermine the public's confidence in the integrity of our biomedical research structure. Examples of such ethical concerns will be discussed with examples of case studies.