The aim of this study was to investigate whether fatty acid profile is a suitable marker for diagnostic purposes in mouse melanoma. Twelve C57Bl/6 male mice were implanted with B16 mouse melanoma cells (106 cells/animal) orthotopically (subcutaneously). After the implantation 4-4 animals were bled by cardiac puncture following narcosis, at days 7, 14, and 21. In order to investigate fatty acid profiles a method based on extraction and HPLC-MS was developed. Signal intensities of 14 fatty acids were determined by mass spectrometry in tumor-free animals as well as tumor bearing animals at the three time points. Mathematical analysis showed non-significant profile changes when control (tumor-free) animals were compared to tumor-implanted ones as well as during tumor progression on week 1, 2 and 3. In case of three fatty acids (myristic acid, palmitoleic acid and eicosadienoic acid) a trend was observed during tumor progression but its statistical significance cannot be evaluated without further investigations. The fatty acid profile cannot be used for early diagnoses in mouse melanoma.