Recent advances in the construction of chemiluminescence flow-cells has included high precision milling of channels into a range of different polymer materials, in efforts to maximise the transfer of light from the chemical reaction to the photodetector. However, little is known of the extent that the colour of polymer materials will influence this transfer. This may become increasingly important as chemiluminescence detection zones are integrated with other operations within microfluidic devices or micro total analysis systems (μTAS). Herein, we compare microfluidic flow-cells fabricated from five polymer sheets (clear, white, black, red, blue), using two flow-cell designs (spiral and serpentine), two modes of photodetection, and four chemiluminescence reactions that provide a range of different emission colours. The direct transfer of light from the reaction within the white flow-cell channel to the photodetector made only minor contributions (10%-20%) to the measured intensity, with the majority of the measured light first interacting with the polymer material into which the channels were machined. The extent that the emitted light was absorbed or reflected by the coloured polymer materials was dependent on not only the properties of the polymer, but also the spectral distribution of the chemiluminescence. The changes in chemiluminescence intensities from absorption of light by the flow-cell materials can be accompanied by distortion of the spectral distribution.