Introduction Globally, C. trachomatis is the leading infectious cause of blindness. There is evidence to suggest that trachomatous inflammation may be linked to ocular infection with other pathogenic organisms. Methods Conjunctival swab samples from 472 Tanzanian children who participated in a 4-year longitudinal study were analysed using optimised duplex qPCR assays to assess carriage of H. influenzae, CNS, S. pneumoniae and Adenovirus spp. in each sample. The presence of C. trachomatis (Ct) in the conjunctiva had previously been recorded. Logistic regression analysis, adjusted for age and sex, was performed to identify associations between the prevalence of bacterial infection and (1) progressive scarring trachoma, and (2) active trachoma (defined as the presence of follicular trachoma (TF) or trachomatous inflammation (TI)). Results Logistic regression identified no significant associations between (1) progressive scarring trachoma and Ct;and (2) progressive scarring trachoma and non-chlamydial bacterial infection. Active trachoma was only associated with conjunctival infection with H. influenzae. Logistic regression found that patients with ocular H. influenzae infection were more likely to demonstrate clinically-graded active trachoma (TF + TI) (OR = 1.96, 95% CI: 1.11 – 3.56, p = 0.023). Individual analyses of TF or TI and their associations with H. influenzae found (1) a strong association between ocular H. influenzae infection and TF (OR = 2.21, p = 0.0095); (2) no association between ocular H. influenzae infection and TI (OR = 2.19, p = 0.19). Conclusion These results indicate that H. influenzae might contribute to the TF phenotype. TF is widely used to assess population levels of trachoma.