We are leveraging recent advances in rapid nucleic acid amplification chemistries, self-powered microfluidics, and low-cost optoelectronics to develop instrumentation for pathogen genotyping in the developing world. A growing number of correlations are emerging between genetic mutations in pathogens and their infectivity, origin, and drug resistance. Particularly for diseases like tuberculosis, where multi-drug resistance is a growing concern, a rapid diagnostic which could inform prescription decisions for newly diagnosed patients would not only save lives and reduce prolonged sickness but would help slow the emergence of more virulent strains. Additionally, for pathogens such as HIV, there is a need for new assay formats which can inexpensively and quantitativly monitor pathogen load. We have developed a portable instrument which uses disposable microfluidic assay cartridges pre-loaded with lyophilized reagents for genetic amplification of multiple markers. The cartridges can be adapted for a variety of sample types (blood, sputum, saliva). The instrument controls assay temperature and quantitatively monitors real-time fluorescence signals from 96 individual reaction chambers. The platform can be tailored for different economic situations from a quantitative electronic readout to a simple binary readout with the naked eye.