Polymerase chain reaction (PCR) screening for presence of transgenic components in food is becoming a routine method in modern food analysis. To develop a high throughput method for quantitation of the PCR products is needed for automatic industry analysis. Here we described an in situ liquid-phase hybridization (LPH) for PCR-enzyme linked immunoabsorbent assays (PCR-ELISA) that was widely used for quantitation of PCR products. In LPH-PCR-ELISA, the biotinylated PCR product was hybridized with digoxigenin-labeled probes in the PCR reaction mixture immediately after PCR cycles and the hybridizations was incorporated into the PCR program. Subsequent enzyme conversion of substrate gave distinct OD values when detecting samples with genetically modified organisms (GMOs) labels in the different concentrations. The described method enabled a fast, specific, and accurate detection of GMOs components in food products and thus can be developed to a full-automatic method for routine analysis of raw and processed food products in large sample number.