The study aims to explore the sensitivity of nanoparticle-assisted polymerase chain reaction (nano-PCR) in alpha 1 and beta 2-microglobulin (MG) detection in urine samples. Three urine MG-positive samples from patients with nephritis, confirmed by a nephelometry immunoassay and conventional reverse transcription (RT)-PCR, were used for a nano-PCR specificity test. Eight dilution series of urine MG-positive samples from patients with nephritis with a ten-fold decrease by sequence (6.25 x 10(7)-6.25 x 10(0) copies/mu L) were chosen for nano-PCR sensitivity verification. Forty-eight selected urine samples with weak positive MG detected using nephelometry immunoassay were tested by the two types of PCR mentioned above. The detection value was compared between the nano-PCR and nephelometry immunoassay in MG detection. As compared to the conventional PCR, nano-PCR had higher specificity and ten-fold higher detection sensitivity. The nano-PCR produced brighter bands and had a higher gene relative expression level than the conventional RT-PCR in the urine sediment specimen with a weak positive MG. The accuracy and sensitivity of nano-PCR were significantly higher than those of the nephelometry immunoassay. Therefore, we believe that nano-PCR may play an important role in the detection of kidney disease in the future.