Introduction: Jar water is a convenient and common source of drinking water in the Kathmandu Valley. However, studies including detailed microbial analyses of this source of potable water are lacking. In this study, jar water samples were examined for the occurrence of Cryptosporidium, Giardia, fecal indicator bacteria, and total bacteria. Methods: Thirty different brands of jars were collected in September 2014. Escherichia coli and total coliforms w ere determined using a Colilert reagent. Ten of the 30 brands w ere selected to test for Cryptosporidium, Giardia, and total bacteria. Bacterial DNA extraction from water samples w as performed using the Cica Geneus DNA Extraction Kit, follow ed by quantitative polymerase chain reaction (qPCR) targeting the 16S rRNA gene of bacterial DNA. Protozoan detection was accomplished by concentrating the samples using the electronegative membrane vortex method, followed by immunomagnetic separation and fluorescent staining. Results: E. coli w as detected in 10% of the samples, with a maximum concentration of 2 most probable number (MPN)/100 mL, whereas total coliforms were detected in 97% of the samples, with a maximum and mean concentration of 7.3 × 10 2 and 3.8 × 10 1 MPN/100 mL, respectively. Total coliforms concentrations in 40% of the samples ranged from 10 2 to 10 3 MPN/100 mL. Cryptosporidium and Giardia w ere not detected in any of the tested samples. Concentrations of total bacteria in the samples ranged from 10 4 to 10 6 cells/100 mL. Conclusions: Ninety-seven percent of the jar water brands were unsuitable for drinking without proper treatment based on the guideline values of the National Drinking Water Quality Standards (NDW Q S) of Nepal. There is no guideline value for total bacteria in NDW Q S however, high concentrations can be indicative of poor control on regrowth of bacteria and recontamination or inefficient water treatment methods.Malla B, Ghaju Shrestha R, Bhandari D, Tandukar S, Shrestha S, Yoshinaga H, Inoue D, Sei K, Nishida K, Tanaka Y, Sherchand JB, Haramoto