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Bio-marker is a substance used as an indicator of a biologic state. It can be defined as any kind of molecule which indicate the existence (past or present) of living organisms. In particular, in the fields of geology and astrobiology biomarkers are also known as biosignatures. In medicine, a biomarkers can be a substance that is introduced in an organism as a means to examine organ function or other aspects of health. For example, rubidium chloride is used as a radioactive isotope to evaluate perfusion of heart muscle. More specifically, a "biomarker" indicates a change in expression or state of a protein that correlates with the risk or progression of a disease, or with the susceptibility of the disease to a given treatment.

However, in environmental science a bio-markers can also be used to indicate exposure to various environmental substances in epidemiology and toxicology. In these cases, the bio-markers may be the external substance itself (e.g. asbestos particles or NNK from tobacco), or a variant of the external substance processed by the body (a metabolite). In genetics, a bio-markers (identified as genetic marker) is a fragment of DNA sequence that causes disease or is associated with susceptibility to disease.

Bio-markers can be used for, Delineation of events between exposure and disease, Establishment of dose-response, Identification of early events in the natural, history Identification of mechanisms by which exposure and disease are related, Reduction in misclassification of exposures or risk factors and disease, Establishment of variability and effect modification and Enhanced individual and group risk assessments.

Environmental bio-markers are bio-molecular signatures--a set of proteins, genes, metabolites, or lipids--that when expressed together present a unique pattern of molecular change in an organism and identify a response to a specific environmental stressor. These signatures may indicate a specific biological response to pollution, subtle changes in the environment, or deliberate releases of toxic substances.

The most important property of environmental bio-marker is its ability to provide an early warning of disease. For example, outbreaks of Avian flu or "bird flu" during the past several years have disrupted the poultry industry. More ominous is that the virus spreads to humans. Now, researchers at Pacific Northwest National Laboratory, through the multi-year Environmental Bio-marker Initiative (EBI), are developing new techniques and tools for identifying these early warning signals also known as environmental bio-marker. Murphy, the lead EBI says "Prediction is the scientific challenge of the 21st century". "And Environmental bio-markers could fundamentally change the way we approach environmental health, assessment, and management. It is a tremendous challenge but very exciting" he continued.

Although, most of the bio-markers are used in medical sciences and epidemiologist, there are several uses of the same in environmental assessment and management. When a disease is suspected of resulting from a toxic exposure, researchers naturally wish to measure the degree of exposure. External exposure is the measured concentration of the toxin in an individual’s immediate environment. While questionnaires offer an historical account of the exposure, direct measurement of the alleged toxin in the air, water, soil, or food can provide accurate information regarding the “dose” of the exposure. Measurement of the external dose provides the basis to understand the relationship to the disease process, but a measurement of “internal” dose may provide more accuracy.

When the toxin is identified in tissues or body fluids it becomes a bio-markers for the internal dose. A bio-marker, that measures a “biologically effective dose” generally indicates the amount of toxin or chemical measured in the target organ or its surrogate. Lead exposure is an excellent example. A history of lead exposure can be strengthened by measurement of lead in the environment, but the best indication of the dose of exposure may be determined in blood and tissues (hair, nails, teeth). The pharmacokinetic properties of the toxin or chemical of interest becomes important to consider in measurement of the internal dose because a number of body fluids could be used based on the pharmacologic properties of the agent. Some chemicals such as halogenated hydrocarbons are stored in adipose tissue but others, such as organophosphate pesticides, are better measured in blood or urine.

Most bio-marker of exposure measure antecedent factors thought to modify (increase or decrease) the risk of developing the disease investigated. The advantage of a bio-marker of exposure over a history of exposure is that it estimates the actual “internal” dose of the exposure. This improves precision in the measurement of any risk factor by adding both internal and external validity when examining the effect of the exposure on the outcome. Bio-markers are particularly useful in the cross-sectional investigation of acute disease because of the pharmacologic properties of the chemical or toxin. It is very difficult to find bio-marker for exposures that are stable over the long periods required for prospective studies of chronic neurological diseases such as Alzheimer’s disease. Banked serum or plasma may be of value in some instances depending on the disorder being investigated and the pharmacologic characteristics of the bio-marker. Issues of timing, persistence, dose, and storage site all must be considered for this class of Bio-markers.