Although epidemiological trends in peanut allergy have been determined, there are limited data for changes in prevalence and clinical characteristics for other common food allergens. This study was performed to determine the trends in prevalence and clinical characteristics of physician-diagnosed pediatric food allergy (FA) at a large urban-based tertiary care center from 2003 to 2008. The electronic medical record system was searched to identify all unique patients with FA as a diagnosis for 2003 and 2008. Included patients had either a definite clinical reaction on ingestion and (1) a positive specific IgE or skin-prick test or (2) food-specific IgE of >90% specificity. Patients with allergies to cow's milk, eggs, fish, peanuts, sesame, shellfish, soy, tree nuts, and wheat were included. The percentage of FA clinic patients increased from 3 to 8% over 5 years. The severity of initial reactions to food also increased from 2003 to 2008 (p < 0.05). Mean initial food-specific IgE decreased from 52 kU/L in 2003 to 40 kU/L in 2003 (p = 0.002). The age at diagnosis decreased from 2003 to 2008 for cow's milk (2.64-1.36 years; p < 0.05) and fish (5.10-2.86 years; p < 0.05) allergies. Peanuts and shellfish were associated with anaphylaxis and severe symptoms in 2008. Clinical characteristics of food-allergic reactions in this large tertiary care center worsened in severity over 5 years and reactions were associated with a lower specific IgE at presentation for peanut and shellfish allergy. Clinical presentation of FA may change over time and this phenomenon warrants study to determine contributory factors.