The photosensitizer protoporphyrin IX, endogenously accumulated from the precursor aminolevulinic acid, is a successful agent in photodynamic tumor therapy. In spite of encouraging clinical results, the basic mechanisms leading to cell death are not fully understood. We therefore set out to analyse the alteration of the gene expression pattern in the squamous cell carcinoma cell line A-431 after photodynamic treatment with endogenous protoporphyrin IX. Radioactively labelled cDNAs from untreated and treated cells were hybridized onto UniGene cDNA array filters containing lysed bacterial colonies with inserts representing approximately 32000 different human transcripts. Differentially expressed genes were identified and verified on sub-arrays containing only the candidate genes. We found increased expression of heat shock protein 70 and of the immediate early genes p55-c-fos and c-jun, may be due to oxidative stress and increased levels of intracellular calcium after photoactivation of protoporphyrin IX. Increased expression of heme oxygenase-1 following dark incubation was not further increased by irradiation and therefore probably caused by the need for heme degradation. Presumably heat shock protein 70 and heme oxygenase-1 serve for cell protection. Though similar results have been found for photodynamic treatment with external porphyrin-based photosensitizers, this is the first report about induction of the genes described above by (photoactivated) endogenous protoporphyrin IX.