The usefulness of near infrared spectroscopy (NIRS) to monitor urine estrogen concentrations was studied in order to determine optimal timing for breeding captive female giant pandas. NIR spectra of daily urine samples from a female giant panda (Ailuropoda melanoleuca) were acquired in the period between March 1st and 25th, 2007 (n= 53). Estrone-3-glucuronide (E1G) concentrations in the samples were also measured by enzyme immunoassay (EIA). Transmittance spectra of all urine samples were obtained in the wavelength range from 1100 to 2432 nm (excluding the range from 1884 to 2012 nm) with sample thickness of 1 mm. Partial least square regression was applied to the spectra and good correlation was obtained between E1G concentration measured by EIA and predicted values by NIR (R2= 0.94, SECV = 10.04 ng ml−1). The results of both soft-independent modeling of class analogy (SIMCA) and moving principal component analysis (MPCA) could detect the time changes in E1G concentration as measured by EIA (the Pearson's correlation coefficients between E1G concentration and the interclass distances of SIMCA or the index of MPCA were r= 0.64 and r= 0.81 respectively, P < 0.01). As for MPCA index, the index sharply dropped on March 24th corresponding to the decrease of the E1G concentration indicating ovulation. Finally, artificial insemination was performed for 3 consecutive days including the peak day, March 24th, and the female became pregnant. These results indicated that NIRS and the following MPCA analysis of the respective urine spectral data could detect the changes of urinary hormones during estrous cycle at a nanogram level. The NIRS can find the optimal timing for breeding quicker and easier than EIA, so this technique can be useful for captive breeding of this threatened species.