Background Superficial basal cell carcinoma (sBCC) and Bowen's disease (BD) are usually slow-growing, low-grade malignancies that mainly affect older persons. Surgery is often the first choice of treatment and the modality with the lowest failure rate. However, non-invasive procedures, such as topical methyl aminolevulinate photodynamic therapy (MAL-PDT) and imiquimod, are increasingly demanded by dermatologists and patients, because of their generally favourable efficacy and adverse effects profile and their excellent cosmetic outcome. Objective To assess the cost of MAL-PDT and of treatment with imiquimod for primary non-melanoma superficial cutaneous carcinomas compared with conventional surgery, thereby calculating the total medical cost, and the direct and indirect costs. Setting We collected data on 67 patients with 86 tumours (32 sBCC, 54 BD). Patients were treated between May 2006 and April 2007 at the Dermatology Department of the Costa del Sol Hospital in Marbella, Spain. The mean cost and mean cost per complete clinical response were calculated for each therapeutic option. Results After 2 years of follow-up, a complete response was observed in 89.5% of the MAL-PDT group, 87.5% of the imiquimod group and 97.5% of the surgery group. The difference in costs when compared with the surgery group was a mean saving per lesion treated of 307 euros for the imiquimod group, and 322 euros for the MAL-PDT group. Conclusions Although surgery proved to be more effective treatment, our results suggest that its average cost is greater than that of non-invasive therapy for the treatment of non-melanoma superficial cutaneous carcinomas on the lower limbs, at least after the first 2 years of follow-up.