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The California Spotted Owl (Strix occidentalis occidentalis ) is under consideration for federal protection and has stimulated ecosystem-level management efforts in Sierra Nevada national forests. Because some populations are declining, we used a noninvasive fecal sampling method to estimate stress hormone (i.e., corticosterone) levels within a local population from April to August 2001. Fecal corticosterone levels were similar to those recorded in a previous study of Northern Spotted Owls (S.o. caurina ) ( &xmacr;= 80.1 ng/g dry feces, SE = 75.8). We then used an information-theoretic approach to identify factors that influence fecal corticosterone levels in Spotted Owls. Our best overall model indicated that nonbreeding owls had higher fecal corticosterone levels than breeding owls early in the breeding season and lower levels later in the breeding season. We collected few samples from breeding owls early in the breeding season, however, which may have influenced the results. Management-related factors reflecting habitat condition and proximity to roads were not correlated with fecal corticosterone. However, factors such as field storage method and sample mass were correlated with the amount of measured fecal corticosterone and should be considered in future studies. Sample vials initially stored on ice had higher levels than those stored immediately in liquid N2 (βstorage= 0.269 ln[ng/g], 95% CI = 0.026, 0.512). Hormone metabolites were extracted from extremely small samples (0.01 g) by slightly modifying the assay protocol, but the amount of corticosterone detected increased as the sample mass decreased (βmass=−6.248 ln[ng/g], 95% CI =−8.877, −3.620). Corticosterone levels were significantly higher in 10 cecal samples collected simultaneously with fecal samples (paired difference = 74.7 ng/g, SE = 45.0, p = 0.001 for a paired t test), so care must be taken to avoid contaminating fecal samples with cecal material. Most of the variation was unexplained by our best model ( R 2= 0.24), and additional factors influencing fecal corticosterone levels need to be identified. Therefore, we recommend that well-designed experiments be conducted under controlled conditions to better determine the effect of factors such as sample handling, partial sampling, and diet on fecal corticosterone levels in owls and other birds. [ABSTRACT FROM AUTHOR]