Background Seasonal allergic conjunctivitis (SAC) and perennial allergic conjunctivitis (PAC) were the most usual types of allergic conjunctivitis. House dust mites were the most common sensitization agents for SAC and PAC. This study aimed to explore SAC and PAC risk factors in children. Methods We recruited 176 children suffering from SAC or PAC and 131 control subjects in southwest China. A questionnaire , several eye exams and  the skin prick test (SPT) were performed.The scores of the symptoms/signs were recorded. Results The percentage of children that had ever been breastfed in the case group was lower than in the control group (P<0.05). The rate of parental allergy history in the case group was higher than for the control group (P<0.01). Compared with the control group, the case group was more likely to have other systemic allergic diseases (P<0.01).The incidence rate  of adenoidal hypertrophy (ATH)  in case group was higher than control group (P<0.05). The ocular symptoms and signs scores had significant correlation to the course (P<0.05), but  no correlation to the SPT results (P>0.05). Conclusion Allergic conjunctivitis may coexist with a variety of allergic diseases, and SAC and PAC may be a risk factor for ATH. Breastfeeding should be recommended, as it may be an alleviating factor for allergic diseases, especially for children of parents with a history of allergic diseases. The disease severity is closely related to its course. Therefore, to avoid difficulty in treatment caused by the aggravation of symptoms and signs, timely antiallergic treatment was recommended.