Indoor air pollution has recently become a public concern in Taiwan. People recognize that indoor air quality (IAQ) may be more important than outdoor air quality because they spend over 80% of their time indoors. IAQ could affect health and comfort of building occupants. The objectives of this study are (1) to characterize the indoor concentrations of selected air pollutants at two hospitals in Hsinchu, Taiwan, (2) to evaluate the potential indoor sources of pollutants in these selected hospitals and their indoor/outdoor relationships, and (3) to compare pollutant concentrations with values published in other studies. A significant between-hospital difference in average indoor concentration of nitrogen dioxide and 54.14, 32.69 ppb for Hospital A and B, respectively (p < 0.05). Indoor nitrogen dioxide concentration was significantly positively correlated with outdoor nitrogen dioxide concentration, PM(10) concentration, and traffic flow (r = 0.91, 0.65 and 0.72, respectively). The ozone level was also lower in our hospitals than 30 ppb standard.