Early diagnosis is crucial for treatment and prognosis of biliary atresia (BA). We used near infrared reflectance spectroscopy (NIRS) for screening of BA. Fecal samples were collected from 200 healthy infants and 16 infants for whom either BA or neonatal hepatitis was diagnosed. Diagnoses were made retrospectively by other diagnostic methods, including laparotomy. The samples (0.5 g each) were manually homogenized. Reflected light from the surface of feces was measured by NIRS. Absorbance peak spectra for fecal fat and conjugated bilirubin were determined before the study, and proved to be 730, 1158, and 1210 nm, respectively. Two cutoff points were set in the second-derivative spectrum: the first (> -0.005) at 730 nm for conjugated bilirubin, and the second (< 1.0) at 1,158:1,210 nm for fat (to include all patients with BA). The sensitivity of NIRS in the diagnosis of BA was 100%, and the specificity was 95.2%. The authors conclude that NIRS is a simple, rapid, noninvasive, and precise technique for the early diagnosis of BA.