Between 1971 and 1980, the use of untreated groundwater was responsible for more than one-third of the waterborne disease outbreaks in the United States. This statistic points to the potential for subsurface contamination by pathogenic microorganisms. The major sources of pathogens are waste water effluents, residual sludges from waste treatment, and septic tank effluents. The number of septic tanks in the United States has been estimated at 22 million units. These on-site treatment systems serve approximately one-third of the U.S. population. They are major contributors to the contamination of subsurface environments. The contaminants are household chemicals (nitrate, heavy metals, organic toxicants), pathogenic microorganisms in soils and aquifer material is primarily governed by their transport and persistence in these environments. The survival and transport of pathogens in soils and aquifers are controlled b four major factors: climate (e.g. temperature, rainfall), type of soil or aquifer material (e.g. texture, pH, water holding capacity, cation exchange capacity), properties of pore fluids (e.g. chemistry, saturation), and type of pathogen. In the following sections, we review the major factors controlling the persistence and transport of pathogens and discuss modeling efforts to assess pathogen fate in soil andsubsurface environments.