Non-attendance for scheduled appointments is common in many medical specialties. However, there are no published reports on non-attendance in pediatric allergy clinics. We investigated the factors for non-attendance in pediatric allergy patients. We assessed the effects of age, gender, ethnic origin, waiting time for an appointment and the timing of the appointment on non-attendance proportions. Chi-square tests were used to analyze statistically significant differences of categorical variables. Logistic regression models were used for multivariate analyses. A total of 442 visits in a 21-month period were included in the study. The overall proportion of non-attendance at the pediatric allergy clinic was 33.0%. Jewish rural patients had 19.4% non-attendance; Jewish urban patients had 35.6% non-attendance; and Bedouin patients had 57.1% non-attendance (p < 0.001). Non-attendance was higher in spring and winter (43.5% and 36.7%, respectively) than in summer and autumn (26.9% and 26.5%, respectively) (p = 0.016). Non-attendance was not significantly influenced by gender, age, hour of the appointment or waiting time for the appointment. A multivariate logistic regression model demonstrated that the ethnic origin of the patients and the season of the year were significantly associated with non-attendance. We conclude that in children attending allergy clinics, factors that determine non-attendance include the ethnic origin of the patients and the season of the year.