Usually case reports of suspected adverse reactions may be influenced by all sorts of bias. The interpretation of pharmacovigilance data may be difficult. Often signals are unsubstantiated and require further study for confirmation or refutation (hypothesis testing) and for the assessment of the reaction frequency, for example, as needed for drug regulatory decision-making.

On the one hand a pharmacovigilance centre has the task to stimulate the use of the collected data by healthcare professionals, and on the other hand to ensure that the heterogeneous and largely unproven data are used in a careful and scientifically (and socially) responsible way.

The spontaneous reporting system is especially helpful in the detection of adverse reactions that are specific or occur in a suggestive time-relationship with drug use (e.g. anaphylactic shock), but may be less effective in studying other sorts of adverse reactions (e.g. cancer development). The potential of the spontaneous reporting system to determine the true frequency of adverse reactions is limited.

The detailed reporting of histories of patients with iatrogenic injury and the subsequent use of the reports are to a variable extent subject to rules regarding privacy and medical secrecy. Confidentiality of personal data is needed. The complex of details in a patient history may be as personal as a finger print and therefore a potential identifier. It is advisable for a pharmacovigilance centre to establish data-management protocols, identifying legitimate data-users and describing which data elements are available to whom and for which purpose and which uses are excluded. Confidentiality primarily concerns the secrecy of the identity of all individuals (patient, reporter, doctor) and institutions (hospital) involved. In many countries case report summaries are not considered confidential.

Besides legal obligations, the basis of spontaneous monitoring is the commitment of healthcare practitioners and patients together to make information available. If pharmacovigilance data were used against the wish of reporters, the system as a whole might collapse.