Background Ocular surface squamous neoplasia (OSSN) is the most common cause of malignancy of the conjunctiva. Variable clinical presentation means that invasive malignant OSSN is often difficult to discriminate from other similarly presenting differential diagnoses which can be managed more conservatively.

Aims Identification of clinical factors associated with a histopathological diagnosis of conjunctival squamous cell carcinoma (SCC).

Methods Prospective consecutive case series of suspected OSSN cases presenting at two hospitals in Central Malawi over a 1 year period. A pro forma was completed assessing preidentified clinical variables. Suspected lesions underwent excisional biopsy followed by histopathological investigation.

Results Fifty-eight patients were recruited. Mean age was 35.8 (range 22–62). 51 cases of histopathologically confirmed OSSN were found. 30 (50%) patients were confirmed HIV seropositive which rose to 86.67% in invasive SCC. Larger size of tumour (p=0.008), male gender (p=0.025) and HIV seropositivity (p=0.010) were associated with invasive SCC pathology.

Conclusions A clinicopathological study of OSSN has not previously been performed in Malawi. The association of HIV with SCC corresponds to previous reports from sub-Saharan Africa. A new finding in our study is a relationship between larger tumour size and invasive lesions confirmed by histopathology. When integrated into a clinical decision-making model, tumour area provides a simple clinical measure for ophthalmic practitioners to use in order to differentiate higher risk OSSN from more benign pathology. The higher risk lesions can subsequently be treated with greater surgical care and undergo closer follow-up.