Background A variety of protocols exist for the treatment of Bowen’s disease by photodynamic therapy (PDT) using topical 5-aminolaevulinic acid (5-ALA). Objective To determine the optimal wavelength (red or green light) for this treatment. Methods A randomized comparison study of ALA–PDT using red (630 ± 15 nm) or green (540 ± 15 nm) light in the treatment of Bowen’s disease. Results The initial clearance rate for lesions treated by red light was 94% (30 of 32) in comparison with 72% (21 of 29) for those lesions receiving green light (P = 0·002). Over the following 12 months, there were two recurrences in the red light group and seven in the green light group reducing the clearance rates to 88% and 48%, respectively. The frequency and severity of pain experienced were similar between the two treatment groups. No hyperthermia, nor significant difference in lesional temperatures, was observed between the wavelengths studied. Conclusion Green light is less effective than red light, at a theoretically equivalent dose, in the treatment of Bowen’s disease by topical ALA–PDT.