Tryptase is useful as a specific and accurate indicator of mast cell activation, whereas histamine, a mast cell's major mediator, also exists in basophils. The aim of this study is to investigate histamine and tryptase levels in allergic conjunctiva. We measured histamine and tryptase levels in conjunctival epithelial cell suspension of children with allergic conjunctivitis (AC) and vernal kerato-conjunctivitis (VKC), and controls, and we evaluated correlations with clinical observations. Both the histamine and tryptase levels in VKC were significantly higher than controls (p < 0.05, p < 0.01), and histamine levels in VKC was also greater than AC (p < 0.05). The histamine/tryptase (H/T) ratios were 0.03 +/- 0.04 in AC, 0.08 +/- 0.09 in VKC and 0.006 +/- 0.006 in controls. The H/T ratios in VKC were significantly higher than controls (p < 0.05) and AC (p < 0.05), and were also found to correlate with the superficial punctate keratopathy (SPK) score (r2 = 0.89). Analyzing the histamine and tryptase levels in conjunctival epithelium may be useful in evaluating the allergic ocular surface, especially in the cases with SPK, where the increase in the histamine levels is not accompanied by an increase in tryptase levels. This suggests an important role for inflammatory cells such as basophils infiltrating into the conjunctival epithelium in allergic reactions.