Conflicts of interest threaten the objectivity of an investigator. Virtually all research projects require judgments to be made. Decisions about what data to collect, how to collect it, and when to exclude portions of a data set from analysis, etc., all require the investigator to use his or her expertise and training in the field.

A conflict of interest can influence the decision-making process. It is important to recognize that having a conflict of interest or a potential conflict does not imply the intent to commit fraud or to deceive. For instance, an investigator who owns stock in a company that develops pesticides may either consciously or unconsciously slant experimental results in favor of the effectiveness or safety of the product. One reason for conflict of interest policies is to avoid unconscious bias.

Conflicts of interest may also threaten public confidence in the research, especially in the case of poorly managed or belatedly-disclosed conflicts. A public that becomes increasingly cynical about the objectivity and the quality of research will rely less on the results of carefully conducted research and more on unsubstantiated or anecdotal evidence in decision making.

For instance, there has been increasing interest among the public in recent years in alternative medical treatment (such as herbal remedies). Rightly or wrongly, it is clear that overall there have been fewer studies of alternative therapies than of conventional therapies. Hence, there is not as much data to support (or deny) the effectiveness of alternative therapies as compared to conventional therapies. Is it possible that the increasing use of alternative therapies is a result of concern by some that ties between doctors and the traditional medical industry are so strong as to cloud objectivity?