BioFETs (biologically sensitive field-effect transistors) are field- effect biosensors with semiconducting transducers. Their device structure is similar to a MOSFET, except that the gate structure is replaced by an aqueous solution containing the analyte. The detection mechanism is the conductance modulation of the transducer due to binding of the analyte to surface receptors. The main advantage of BioFETs, compared to currently available technology, is label-free operation. We present a quantitative analysis of BioFETs which is centered around multi-scale models. The technique for solving the multi-scale problem used here is the derivation of interface conditions for the Poisson equation that include the effects of the quasi-periodic biofunctionalized boundary layer. The multi- scale model enables self-consistent simulation and can be used with any charge transport model. Hence it provides the foundation for understanding the physics of the sensors by continuum models.