The aim of the study was to compare the expression of oestrogen receptor alpha (ERα) in neovaginal tissue of patients with vaginal agenesis following neovaginoplasty using regenerated, oxidised cellulose in premenopausal women. A prospective, observational case-control study was performed on eight patients with vaginal agenesis following modified Abbé-McIndoe neovaginoplasty and 10 control premenopausal women following benign gynaecologic surgery. 6F11 monoclonal antibody was used to determine ERα expression in the vaginal mucosa. Quantitative and qualitative evaluations were performed, respectively, in vaginal epithelium and stroma. The thickness of the vaginal epithelium was determined as the vertical distance between the basal layer cells and the apical surface of the superficial layer. The percentage of ERα-expressing cells was higher in the control group, except in the superficial zone of the epithelium. In the stromal tissue, ERα was detected in only one patient from the neovagina group compared with nine women in the control group. The neovagina group had a statistically thinner epithelium. Our study suggests that women with vaginal agenesis following modified Abbé-McIndoe neovaginoplasty using regenerated oxidised, cellulose experience relatively local hypo-oestrogenism in the first year after surgery, with repercussion in vaginal trophism.