We review issues related to the inclusion of biospecimens in epidemiological studies. Technical advances and the revolution in molecular biology have rendered the use of biomarkers increasingly feasible in epidemiological investigations, however the cost and complexity require interdisciplinary expertise and careful attention to methodological detail in order to ensure validity. The widespread banking of biospecimens for long-term (cohort) studies requires special attention to be paid to these issues. Blood, urine and tumour tissue are in common use in medicine and at least some aspects of sample handling derives directly from this clinical experience, although special considerations apply in the epidemiological setting. An increasingly broad array of biospecimen types have been studied, including exhaled air, nail clippings, buccal cells, saliva, semen, faeces and breast milk. Relevant issues in the processing, storage, shipping, timing of collection and safety procedures are examined in terms of their potential to distort results. The role of carefully developed quality control protocols is emphasized. In order to take full advantage of the opportunities afforded by the use of biomarkers in epidemiological studies, careful attention to biospecimen processing, the stability of the biomarker and the precautions to be taken during transportation and storage of samples is necessary.