OBJECTIVE To evaluate goblet cell density (GCD) on conjunctiva and cornea in patients with ocular chemical burns by in vivo laser scanning confocal microscopy (LSCM) and impression cytology (IC) and to explore the correlation between two methods. METHODS Fifty-four patients (58 eyes) with chemical burn were enrolled in the study. LSCM was applied to identify the goblet cells on conjunctiva and cornea under in vivo conditions, and GCD was analyzed with the customized software. Impression cytology was then performed, and the biopsy specimens were stained to visualize goblet cells in vitro and to measure the density. Statistical software was used to analyze the correlation between GCD taken by two methods. RESULTS Conjunctival goblet cells could be discriminated in 55 eyes and 57 eyes by in vivo LSCM and IC. They could be identified on the cornea in nine eyes and eight eyes by two methods. The positive rate of two methods had no significant difference. GCDs on conjunctiva measured by in vivo LSCM and IC were 136 +/- 79 cells/mm(2) and 121 +/- 66 cells/mm(2). Median GCDs on cornea detected by two methods were 30 cells/mm(2) and 23 cells/mm(2), respectively. A significant positive correlation was found between the GCDs on conjunctiva measured by these two methods as well as the GCDs on cornea. CONCLUSIONS GCD decreased in patients with chemical burns. A positive correlation was found between GCD measured by in vivo LSCM and IC after chemical burns. In vivo LSCM was a promising device to study goblet cells in vivo under pathologic conditions.