The choice of the growth substrate for cell cultures used in fluorescence microscopy is guided by several factors including the type of cells studied and the type of microscopy used. Usually, cells can be cultured on either polymer or glass substrates. One type of polymer, termed Aclar, presents several attractive features: the adhesive properties are better than those of glass, the optical properties are comparable to those of glass, it is biochemically inert, unbreakable, flexible and has a high surface tension, convenient for seeding cells on the cover slip. However, here we show that when imaging with two-photon microscopy, which is based on a femtosecond pulsed laser source, local damage of the Aclar substrate occurs, starting at an average intensity of 10(5) W cm(-2) at the focal point and for exposure times insufficient to cause cell damage. This leads to the appearance of gas bubbles on cultures plated on Aclar cover slips, which perturb the imaging. By contrast, this phenomenon does not occur on borosilicate cover slips, probably because of their different physical (thermal conductivity, absorbance, melting point) and material homogeneity properties. Thus, for cell culture applications using pulsed lasers with high intensities, the use of glass is preferable to Aclar. The results also reveal that substrates can be more susceptible to thermal damage than the cells themselves.