Male-specific coliphages (FRNA) have been used as fecal indicators and possible viral indicators for various water matrices such as surface, ground, and drinking water. US Environmental Protection Method Method 1602 has been validated to detect and enumerate FRNA coliphages from groundwater. However, it requires 18-24 hr incubation period and may not be suitable for emerging detection of fecal contamination in drinking water. Real-time PCR is one of the latest developed technologies that have been used in clinical microbiology to rapidly detect and quantify microorganisms successfully. It allows real time monitoring on the amplification process and quantifying the fluorescent labeled amplicons in each cycle. The emitted fluorescent signal increases in direct proportion to the amount of amplicons in a reaction. This study explores the possibility of rapidly quantifying FRNA coliphages in river and raw water using real-time PCR. One mL raw water was spiked with a reference strain of coliphages MS2, followed by passing through size exclusion-ion exchange column prior to real-time RT-PCR reaction. The chelax-100 and sephedex-100, size exclusion-ion exchange column was found to effectively remove PCR inhibitors in raw water because no coliphage MS2 was detected without treated with the chelax-sephedex column. The detection sensitivity of the real-time RTPCR developed was 10 PFU per reaction. The primers were specific to detect all strains of FRNA but not FDNA and somatic coliphages. Of the eight river water and twelve raw water samples collected from the Semenyih Treatment Plant, Selangor over the period of 5 months, 40% of the samples were positive for FRNA with a range from 1 to 12 PFU/reaction by real-time RT-PCR, but were enumerated with plaque counts ranged from 2 to 44 PFU/100ml by plaque analysis. Includes table, figures.