Indoor and outdoor endotoxin in PM2.5 was measured for the very first time in Santiago, Chile, in spring 2012. Average endotoxin concentrations were 0.099 and 0.094 [EU/m3] for indoor (N=44) and outdoor (N=41) samples, respectively; the indoor–outdoor correlation (log-transformed concentrations) was low: R=−0.06, 95% CI: (−0.35 to 0.24), likely owing to outdoor spatial variability.A linear regression model explained 68% of variability in outdoor endotoxins, using as predictors elemental carbon (a proxy of traffic emissions), chlorine (a tracer of marine air masses reaching the city) and relative humidity (a modulator of surface emissions of dust, vegetation and garbage debris). In this study, for the first time a potential source contribution function (PSCF) was applied to outdoor endotoxin measurements. Wind trajectory analysis identified upwind agricultural sources as contributors to the short-term, outdoor endotoxin variability. Our results confirm an association between combustion particles from traffic and outdoor endotoxin concentrations.For indoor endotoxins, a predictive model was developed but it only explained 44% of endotoxin variability; the significant predictors were tracers of indoor PM2.5 dust (Si, Ca), number of external windows and number of hours with internal doors open. Results suggest that short-term indoor endotoxin variability may be driven by household dust/garbage production and handling. This would explain the modest predictive performance of published models that use answers to household surveys as predictors. One feasible alternative is to increase the sampling period so that household features would arise as significant predictors of long-term airborne endotoxin levels.