AIM: To analyze the lab diagnosis and etiology of infectious endophthalmitis. METHODS: The medical and microbial records of 36 patients diagnosed with infectious endophthalmitis and 8 patients diagnosed with intraocular lens (IOL)-related inflammation between Nov. 1999 and Dec. 2009 were retrospectively reviewed for lab diagnosis and etiology. RESULTS: The inflammatory cell counts in all aqueous humor specimens from infectious endophthalmitis patients were more than in all aqueous humor specimens from patients with IOL-related inflammation. Sixteen of the 36 aqueous humor samples (44.4%) and 11 of the 24 vitreous humor samples (45.8%) from infectious endophthalmitis patients showed positive results in smears; while 17 aqueous humor samples (47.2%) and 15 vitreous humor samples (62.5%) from infectious endophthalmitis patients showed positive results in culture. CONCLUSION: The inflammatory cell count may be an important index for infectious endophthalmitis; while, smears can show etiological information earlier.