Introduction The host cellular immune response plays an integral role in controlling human papilloma virus (HPV)-induced precancerous lesions. Anal mucosal cellular immune responses have not been previously studied. Methods The Study of the Prevention of Anal Cancer (SPANC) is a longitudinal natural history study of anal HPV infection in men ≥35 years who have sex with men. 26 participants with anal, high-grade (grade 2 or 3) squamous intraepithelial lesions (HSIL) at study entry had 44 anal biopsies. Lymphoid aggregates in these biopsies were detected by inspection of haematoxylin and eosin-stained sections. Additional sections were immunofluorescently stained to enumerate submucosal and intra-epithelial CD4 + and CD8 + T-cell counts. Whole slide imaging to reveal full tissue architecture at high resolution (x600) was used. Student’s t-test of log 10 -transformed T-cell density was used to compare means; a generalised, linear model was used to determine factors associated with total T-cell density (biopsy-based analysis with intra-subject adjustment). Results Of 26 men with mean age 53 years [standard deviation (SD) 10.5], 7 (27%) were HIV-infected and 17 (68%) had concurrent anal HPV16 in anal swabs. Of 44 biopsies, 26 (59%) revealed HSIL and 24 (55%) had lymphoid aggregates localised in the submucosa adjacent to the epithelium. Presence of lymphoid aggregates was associated with higher CD4 + T-cell density (mean 192 vs. 69 cells/mm 2 , P + T-cell density (106 vs. 62 cells/mm 2 , P = 0.077). A biopsy diagnosed with HSIL was significantly associated with higher total T-cell density [odds ratio (OR) 11.80, 95% confidence interval (CI) 1.51 – 92.08, P = 0.02], as was having anal HPV16 detected (OR 14.08, 95% CI 1.15 – 172.71, P = 0.04). Presence of low-risk HPV genotype (s) was not associated (OR 1.37, 95% CI 0.12 – 15.14, P = 0.80). Conclusion CD4 + T-cell enriched lymphoid aggregates in the anal mucosa were associated with anal HSIL and HPV 16. Disclosure of interest statement Winnie Tong and Jennifer Roberts declare no conflicts of interest. This work was supported by the St Vincent’s Clinic Foundation K&A Collins Cancer Grant 2014. The SPANC study is funded by the National Health and Medical Research Council Program (grant 568971) and the Cancer Council New South Wales Strategic Research Partnership (grant SRP13–11).