Background Pandemic influenza A (H1N1) virus emerged during 2009. To help clinicians triage adults with acute respiratory illness, a scoring system for influenza-like illness (ILI) was implemented at Hospital Civil de Guadalajara, Mexico. Methods A medical history, laboratory and radiology results were collected on emergency room (ER) patients with acute respiratory illness to calculate an ILI-score. Patients were evaluated for admission by their ILI-score and clinicians' assessment of risk for developing complications. Nasal and throat swabs were collected from intermediate and high-risk patients for influenza testing by RT-PCR. The disposition and ILI-score of those oseltamivir-treated versus untreated, clinical characteristics of 2009 pandemic influenza A (H1N1) patients versus test-negative patients were compared by Pearson's Χ2, Fisher's Exact, and Wilcoxon rank-sum tests. Results Of 1840 ER patients, 230 were initially hospitalized (mean ILI-score = 15), and the rest were discharged, including 286 ambulatory patients given oseltamivir (median ILI-score = 11), and 1324 untreated (median ILI-score = 5). Fourteen (1%) untreated patients returned, and 3 were hospitalized on oseltamivir (median ILI-score = 19). Of 371 patients tested by RT-PCR, 104 (28%) had pandemic influenza and 42 (11%) had seasonal influenza A detected. Twenty (91%) of 22 imaged hospitalized pandemic influenza patients had bilateral infiltrates compared to 23 (38%) of 61 imaged hospital test-negative patients (p<0.001). One patient with confirmed pandemic influenza presented 6 days after symptom onset, required mechanical ventilation, and died. Conclusions The triaging system that used an ILI-score complimented clinicians' judgment of who needed oseltamivir and inpatient care and helped hospital staff manage a surge in demand for services.