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Aims To assess the potential impact on long-term consequences of treatment (intensity-modulated radiotherapy with concomitant chemotherapy) in patients diagnosed with anal cancer. Materials and methods We identified 43 eligible patients treated with concomitant chemoradiotherapy (pelvic intensity-modulated radiotherapy) at the Royal Marsden Hospital between 2010 and 2013. We determined late genitalia and bowel side-effects using specific questionnaires [Pelvic Symptom Questionnaire, Vaizey Incontinence Questionnaire, Inflammatory Bowel Disease Questionnaire (IBDQ) and IBDQ-B]. Using descriptive statistics, we report clinical outcomes in all patients, by time, since the end of treatment (grouped as 1–1.5, 1.5–2.5 and 2.5–3.5 years). Results Twenty-seven of 43 (63%) patients were identified as available for questionnaire follow-up. Reasons for unavailability were death ( n = 3), lost to palliative care service ( n = 1), referred to surgery ( n = 4), lost to follow-up ( n = 8). In the 27 patients studied, bowel toxicity was assessed by IBDQ, IBDQ-B and the Vaizey Incontinence Questionnaire. The median value was 208 for IBDQ, 38 for IBDQ-B and 3.0 for the Vaizey Incontinence Questionnaire, as assessed at 1 year or more post-completion of treatment. Treatment was reported to affect quality of life/sexual function in two of the female patients ( n = 21) and three male patients ( n = 6). No insufficiency fractures have been reported. Bone marrow function remained stable over the time of the follow-up. Conclusions Although there are data supporting a reduction in acute effects using intensity-modulated radiotherapy in anal cancer, there is very little in the literature to establish the late toxicity profile. Our results indicate that there is an effect on bowel and sexual function, but it does not increase over the period observed. These data provide a benchmark against which to compare outcomes with future manipulation in treatment, and provide us with real information to give patients as to the expectation of their functional outcome after treatment. [ABSTRACT FROM AUTHOR]