This current study presents a new miniature, integrated system capable of rapid detection of genetic deletion from saliva samples. Several critical modules including a genomic DNA (gDNA) extraction module, a polymerase chain reaction (PCR) module, and an external optical detection module are integrated into the system. Silica-modified magnetic beads are first incubated with saliva in an extraction chamber with a cell lysis solution. This is followed by the collection of released gDNA onto the surface of the microbeads, which is then further purified and concentrated utilizing a magnetic field generated by an on-chip array of microcoils. Then, genetic deletion of human genes can be specifically amplified by the on-chip PCR module and is immediately detected using the optical detection module. Experimental results show that high-quality gDNA with an average concentration of 50.45 ng/microL can be extracted from 100 microL of saliva. The detection of a mutated alpha-globin gene associated with alpha-thalassemia-1 of southeast Asian (SEA)-type deletion can be completed within less than 1 h. Moreover, the detection limit of the system is found to be 12.00 pg/microL with a high sensitivity up to 90%. Consequently, the proposed saliva-based miniature system can provide a powerful platform for rapid DNA extraction and detection of genetic diseases.