The serum- and glucocorticoid-inducible kinase 1 (SGK1) is a key-regulator of transport, cell volume and cell survival. SGK1 transcription is under genomic control of a wide variety of hormones and cell stressors. Little is known, however, about sequence variation in SGK1 transcripts. Thus, we took an in silico approach to determine sequence variations in the N-terminal region of SGK1, which is considered particularly important for subcellular SGK1 localization. Expressed Sequence Tag analysis revealed two novel phylogenetically highly conserved SGK1 mRNAs with different promoter sites based on alternative initiation of transcription at -2981, -850 upstream of the transcription initiation site (+1) of the reference mRNA. RT-PCR in various human cell lines and tissues confirmed the expression of the 3 alternative splice variants, which differed exclusively in their first exons. The two novel variants were devoid of the localization and degradation signal with otherwise unchanged and intact open reading frames. Spatial distribution of transcription factor binding sites among the three promoter sites indicated common responsiveness to glucocorticoids but different responsiveness to hypoxia and cellular differentiation. Differential expression under those conditions was confirmed for all variants in cultured myoblasts and myotubes. p53 and ETF-1 binding sites were overrepresented at the promoter site of the reference sequence variant SGK1(+1). Transcript levels were 4.1-fold [SGK1(+1)] and 3.1-fold [SGK1(-850)] higher in renal clear cell carcinoma than in remote tissue. The transcript levels were 42-fold [SGK1(+1)], 26-fold [SGK1(-850)] and 17-fold [SGK1(-2981)] higher in highly malignant human glioma cells than in non-neoplastic brain tissue. SGK1 transcript levels were differentially increased by differentiation or hypoxia (treatment with CoCl(2)). In conclusion, the present observations disclose the transcription of three distinct SGK1 splice variants, which are all markedly upregulated in tumor tissue but differentially upregulated following differentiation or hypoxia.