Conjunctivitis is a very common presentation to general practitioners and general paediatricians. The investigation of conjunctivitis can be a significant cost to microbiology laboratories due to the high volume of samples that can be submitted, particularly from patients in the community. The key issue is to send eye swabs in clinical situations where it can make a difference to management, and limiting the use of eye swabs in routine cases of conjunctivitis which are likely to be due to viruses. For investigation of neonatal conjunctivitis we recommend sending a bacterial swab for routine culture, and also a swab for molecular detection of Chlamydia trachomatis and Neisseria gonorrhoeae. In older children with mild conjunctivitis no swab is necessary unless there is marked conjunctival injection. In this article we also highlight patient populations that require specialist tests to be sent as part of their assessment such as contact lens wearers and sexually active teenagers.